Merge pull request #175 from Liujingfang1/crd

skip adding namespace to CustomResourceDefinitions

.travis.yml

@@ -12,6 +12,8 @@ before_install:
   - go get -u golang.org/x/tools/cmd/goimports
   - go get -u github.com/onsi/ginkgo/ginkgo
   - go get -u github.com/monopole/mdrip
+  - go get -u github.com/fzipp/gocyclo
+  - go get -u gopkg.in/alecthomas/gometalinter.v2 && gometalinter.v2 --install
 
 # Install must be set to prevent default `go get` to run.
 # The dependencies have already been vendored by `dep` so

CONTRIBUTING.md

@@ -16,7 +16,7 @@
 1. Fork the repo, develop and test your code.
    See the [github workflow guide].
 1. For _new features_, provide a markdown-based demo following
-   the pattern established in the [demos](demos) directory.
+   the pattern established in the [examples](examples) directory.
    Run `bin/pre-commit.sh` to test your demo.
 1. Submit a pull request.
 

Gopkg.lock

@@ -1,12 +1,33 @@
 # This file is autogenerated, do not edit; changes may be undone by the next 'dep ensure'.
 
 
+[[projects]]
+  name = "github.com/PuerkitoBio/purell"
+  packages = ["."]
+  revision = "0bcb03f4b4d0a9428594752bd2a3b9aa0a9d4bd4"
+  version = "v1.1.0"
+
+[[projects]]
+  branch = "master"
+  name = "github.com/PuerkitoBio/urlesc"
+  packages = ["."]
+  revision = "de5bf2ad457846296e2031421a34e2568e304e35"
+
 [[projects]]
   name = "github.com/davecgh/go-spew"
   packages = ["spew"]
   revision = "346938d642f2ec3594ed81d874461961cd0faa76"
   version = "v1.1.0"
 
+[[projects]]
+  name = "github.com/emicklei/go-restful"
+  packages = [
+    ".",
+    "log"
+  ]
+  revision = "3658237ded108b4134956c1b3050349d93e7b895"
+  version = "v2.7.1"
+
 [[projects]]
   name = "github.com/evanphx/json-patch"
   packages = ["."]
@@ -19,9 +40,36 @@
   revision = "0ca9ea5df5451ffdf184b4428c902747c2c11cd7"
   version = "v1.0.0"
 
+[[projects]]
+  branch = "master"
+  name = "github.com/go-openapi/jsonpointer"
+  packages = ["."]
+  revision = "3a0015ad55fa9873f41605d3e8f28cd279c32ab2"
+
+[[projects]]
+  branch = "master"
+  name = "github.com/go-openapi/jsonreference"
+  packages = ["."]
+  revision = "3fb327e6747da3043567ee86abd02bb6376b6be2"
+
+[[projects]]
+  branch = "master"
+  name = "github.com/go-openapi/spec"
+  packages = ["."]
+  revision = "bcff419492eeeb01f76e77d2ebc714dc97b607f5"
+
+[[projects]]
+  branch = "master"
+  name = "github.com/go-openapi/swag"
+  packages = ["."]
+  revision = "811b1089cde9dad18d4d0c2d09fbdbf28dbd27a5"
+
 [[projects]]
   name = "github.com/gogo/protobuf"
-  packages = ["proto","sortkeys"]
+  packages = [
+    "proto",
+    "sortkeys"
+  ]
   revision = "1adfc126b41513cc696b209667c8656ea7aac67c"
   version = "v1.0.0"
 
@@ -33,7 +81,13 @@
 
 [[projects]]
   name = "github.com/golang/protobuf"
-  packages = ["proto","ptypes","ptypes/any","ptypes/duration","ptypes/timestamp"]
+  packages = [
+    "proto",
+    "ptypes",
+    "ptypes/any",
+    "ptypes/duration",
+    "ptypes/timestamp"
+  ]
   revision = "b4deda0973fb4c70b50d226b1af49f3da59f5265"
   version = "v1.1.0"
 
@@ -45,7 +99,11 @@
 
 [[projects]]
   name = "github.com/googleapis/gnostic"
-  packages = ["OpenAPIv2","compiler","extensions"]
+  packages = [
+    "OpenAPIv2",
+    "compiler",
+    "extensions"
+  ]
   revision = "ee43cbb60db7bd22502942cccbc39059117352ab"
   version = "v0.1.0"
 
@@ -61,6 +119,16 @@
   revision = "ca39e5af3ece67bbcda3d0f4f56a8e24d9f2dad4"
   version = "1.1.3"
 
+[[projects]]
+  branch = "master"
+  name = "github.com/mailru/easyjson"
+  packages = [
+    "buffer",
+    "jlexer",
+    "jwriter"
+  ]
+  revision = "3fdea8d05856a0c8df22ed4bc71b3219245e4485"
+
 [[projects]]
   name = "github.com/modern-go/concurrent"
   packages = ["."]
@@ -73,6 +141,12 @@
   revision = "1df9eeb2bb81f327b96228865c5687bc2194af3f"
   version = "1.0.0"
 
+[[projects]]
+  name = "github.com/pkg/errors"
+  packages = ["."]
+  revision = "645ef00459ed84a119197bfb8d8205042c6df63d"
+  version = "v0.8.0"
+
 [[projects]]
   name = "github.com/spf13/cobra"
   packages = ["."]
@@ -88,12 +162,33 @@
 [[projects]]
   branch = "master"
   name = "golang.org/x/net"
-  packages = ["http/httpguts","http2","http2/hpack","idna"]
+  packages = [
+    "http/httpguts",
+    "http2",
+    "http2/hpack",
+    "idna"
+  ]
   revision = "2491c5de3490fced2f6cff376127c667efeed857"
 
 [[projects]]
   name = "golang.org/x/text"
-  packages = ["collate","collate/build","internal/colltab","internal/gen","internal/tag","internal/triegen","internal/ucd","language","secure/bidirule","transform","unicode/bidi","unicode/cldr","unicode/norm","unicode/rangetable"]
+  packages = [
+    "collate",
+    "collate/build",
+    "internal/colltab",
+    "internal/gen",
+    "internal/tag",
+    "internal/triegen",
+    "internal/ucd",
+    "language",
+    "secure/bidirule",
+    "transform",
+    "unicode/bidi",
+    "unicode/cldr",
+    "unicode/norm",
+    "unicode/rangetable",
+    "width"
+  ]
   revision = "f21a4dfb5e38f5895301dc265a8def02365cc3d0"
   version = "v0.3.0"
 
@@ -112,13 +207,75 @@
 [[projects]]
   branch = "master"
   name = "k8s.io/api"
-  packages = ["admissionregistration/v1alpha1","admissionregistration/v1beta1","apps/v1","apps/v1beta1","apps/v1beta2","authentication/v1","authentication/v1beta1","authorization/v1","authorization/v1beta1","autoscaling/v1","autoscaling/v2beta1","batch/v1","batch/v1beta1","batch/v2alpha1","certificates/v1beta1","core/v1","events/v1beta1","extensions/v1beta1","networking/v1","policy/v1beta1","rbac/v1","rbac/v1alpha1","rbac/v1beta1","scheduling/v1alpha1","settings/v1alpha1","storage/v1","storage/v1alpha1","storage/v1beta1"]
+  packages = [
+    "admissionregistration/v1alpha1",
+    "admissionregistration/v1beta1",
+    "apps/v1",
+    "apps/v1beta1",
+    "apps/v1beta2",
+    "authentication/v1",
+    "authentication/v1beta1",
+    "authorization/v1",
+    "authorization/v1beta1",
+    "autoscaling/v1",
+    "autoscaling/v2beta1",
+    "batch/v1",
+    "batch/v1beta1",
+    "batch/v2alpha1",
+    "certificates/v1beta1",
+    "core/v1",
+    "events/v1beta1",
+    "extensions/v1beta1",
+    "networking/v1",
+    "policy/v1beta1",
+    "rbac/v1",
+    "rbac/v1alpha1",
+    "rbac/v1beta1",
+    "scheduling/v1alpha1",
+    "settings/v1alpha1",
+    "storage/v1",
+    "storage/v1alpha1",
+    "storage/v1beta1"
+  ]
   revision = "53d615ae3f440f957cb9989d989d597f047262d9"
 
 [[projects]]
   branch = "master"
   name = "k8s.io/apimachinery"
-  packages = ["pkg/api/resource","pkg/apis/meta/v1","pkg/apis/meta/v1/unstructured","pkg/conversion","pkg/conversion/queryparams","pkg/fields","pkg/labels","pkg/runtime","pkg/runtime/schema","pkg/runtime/serializer","pkg/runtime/serializer/json","pkg/runtime/serializer/protobuf","pkg/runtime/serializer/recognizer","pkg/runtime/serializer/versioning","pkg/selection","pkg/types","pkg/util/errors","pkg/util/framer","pkg/util/intstr","pkg/util/json","pkg/util/mergepatch","pkg/util/net","pkg/util/runtime","pkg/util/sets","pkg/util/strategicpatch","pkg/util/validation","pkg/util/validation/field","pkg/util/wait","pkg/util/yaml","pkg/watch","third_party/forked/golang/json","third_party/forked/golang/reflect"]
+  packages = [
+    "pkg/api/resource",
+    "pkg/apis/meta/v1",
+    "pkg/apis/meta/v1/unstructured",
+    "pkg/conversion",
+    "pkg/conversion/queryparams",
+    "pkg/fields",
+    "pkg/labels",
+    "pkg/runtime",
+    "pkg/runtime/schema",
+    "pkg/runtime/serializer",
+    "pkg/runtime/serializer/json",
+    "pkg/runtime/serializer/protobuf",
+    "pkg/runtime/serializer/recognizer",
+    "pkg/runtime/serializer/versioning",
+    "pkg/selection",
+    "pkg/types",
+    "pkg/util/errors",
+    "pkg/util/framer",
+    "pkg/util/intstr",
+    "pkg/util/json",
+    "pkg/util/mergepatch",
+    "pkg/util/net",
+    "pkg/util/runtime",
+    "pkg/util/sets",
+    "pkg/util/strategicpatch",
+    "pkg/util/validation",
+    "pkg/util/validation/field",
+    "pkg/util/wait",
+    "pkg/util/yaml",
+    "pkg/watch",
+    "third_party/forked/golang/json",
+    "third_party/forked/golang/reflect"
+  ]
   revision = "13b73596e4b63e03203e86f6d9c7bcc1b937c62f"
 
 [[projects]]
@@ -130,18 +287,15 @@
 [[projects]]
   branch = "master"
   name = "k8s.io/kube-openapi"
-  packages = ["pkg/util/proto"]
+  packages = [
+    "pkg/common",
+    "pkg/util/proto"
+  ]
   revision = "b3f03f55328800731ce03a164b80973014ecd455"
 
-[[projects]]
-  branch = "master"
-  name = "k8s.io/utils"
-  packages = ["exec"]
-  revision = "258e2a2fa64568210fbd6267cf1d8fd87c3cb86e"
-
 [solve-meta]
   analyzer-name = "dep"
   analyzer-version = 1
-  inputs-digest = "6e36daa1798b0dae7f45160f9275ca6bbe6c5667de7cd808d0057cbaf19fc55e"
+  inputs-digest = "586d4cb9094e9b5c0731f16e931b953e9c0f709b7125a7537ae3625ada179eee"
   solver-name = "gps-cdcl"
   solver-version = 1

Gopkg.toml

@@ -52,3 +52,7 @@
 [[constraint]]
   branch = "master"
   name = "k8s.io/utils"
+
+[[constraint]]
+  branch = "master"
+  name = "github.com/go-openapi/spec"

INSTALL.md

@@ -0,0 +1,27 @@
+[release page]: https://github.com/kubernetes-sigs/kustomize/releases
+[Go]: https://golang.org
+
+## Installation
+
+Download a binary from the [release page].
+
+Or try this to grab the latest official release
+using the command line:
+
+```
+opsys=linux  # or darwin, or windows
+curl -s https://api.github.com/repos/kubernetes-sigs/kustomize/releases/latest |\
+  grep browser_download |\
+  grep $opsys |\
+  cut -d '"' -f 4 |\
+  xargs curl -O -L
+mv kustomize_*_${opsys}_amd64 kustomize
+chmod u+x kustomize
+```
+
+To install from head with [Go] v1.10.1 or higher:
+
+<!-- @installkustomize @test -->
+```
+go get github.com/kubernetes-sigs/kustomize
+```

README.md

@@ -1,71 +1,141 @@
 # kustomize
 
-[applied]: docs/glossary.md#apply
-[base]: docs/glossary.md#base
-[declarative configuration]: docs/glossary.md#declarative-application-management
-[demo]: demos/README.md
-[demos]: demos/README.md
-[imageBase]: docs/base.jpg
-[imageOverlay]: docs/overlay.jpg
-[kubernetes style]: docs/glossary.md#kubernetes-style-object
-[KEP]: https://github.com/kubernetes/community/blob/master/keps/sig-cli/0008-kustomize.md
-[kustomization]: docs/glossary.md#kustomization
-[overlay]: docs/glossary.md#overlay
-[resources]: docs/glossary.md#resource
-[sig-cli]: https://github.com/kubernetes/community/blob/master/sig-cli/README.md
-[workflows]: docs/workflows.md
+`kustomize` lets you customize raw, template-free YAML
+files for multiple purposes, leaving the original YAML
+untouched and usable as is.
 
-
-`kustomize` is a command line tool supporting
-template-free customization of YAML (or JSON) objects
-that conform to the [kubernetes style].  If your
-objects have a `kind` and a `metadata` field,
-`kustomize` can patch them to support configuration
-sharing and re-use.
-
-For more details, try a [demo].
+`kustomize` targets kubernetes; it understands and can
+patch [kubernetes style] API objects.  It's like
+[`make`], in that what it does is declared in a file,
+and it's like [`sed`], in that it emits editted text.
 
 [![Build Status](https://travis-ci.org/kubernetes-sigs/kustomize.svg?branch=master)](https://travis-ci.org/kubernetes-sigs/kustomize)
 [![Go Report Card](https://goreportcard.com/badge/github.com/kubernetes-sigs/kustomize)](https://goreportcard.com/report/github.com/kubernetes-sigs/kustomize)
 
-
-## Installation
-
-This assumes [Go](https://golang.org/) (v1.10.1 or higher)
-is installed and your `PATH` contains `$GOPATH/bin`:
-
-<!-- @installkustomize @test -->
-```
-go get github.com/kubernetes-sigs/kustomize
-```
-
+**Installation**: Download a binary from the [release
+page], or see these [install] notes. Then try one of
+the tested [examples].
 
 ## Usage
 
-#### 1) Make a base
 
-A [base] configuration is a [kustomization] file listing a set of
-k8s [resources] - deployments, services, configmaps,
-secrets that serve some common purpose.
+### 1) Make a [kustomization] file
+
+In some directory containing your YAML [resource]
+files (deployments, services, configmaps, etc.), create a
+[kustomization] file.
+
+This file should declare those resources, and any
+customization to apply to them, e.g. _add a common
+label_.
 
 ![base image][imageBase]
 
-#### 2) Customize it with overlays
+File structure:
 
-An [overlay] customizes your base along different dimensions
-for different purposes or different teams, e.g. for
-_development, staging and production_.
+> ```
+> ~/someApp
+> ├── deployment.yaml
+> ├── kustomization.yaml
+> └── service.yaml
+> ```
+
+The resources in this directory could be a fork of
+someone else's configuration.  If so, you can easily
+rebase from the source material to capture
+improvements, because you don't modify the resources
+directly.
+
+Generate customized YAML with:
+
+```
+kustomize build ~/someApp
+```
+
+The YAML can be directly [applied] to a cluster:
+
+> ```
+> kustomize build ~/someApp | kubectl apply -f -
+> ```
+
+
+### 2) Create [variants] using [overlays]
+
+Manage traditional [variants] of a configuration - like
+_development_, _staging_ and _production_ - using
+[overlays] that modify a common [base].
 
 ![overlay image][imageOverlay]
 
-#### 3) Run kustomize
+File structure:
+> ```
+> ~/someApp
+> ├── base
+> │   ├── deployment.yaml
+> │   ├── kustomization.yaml
+> │   └── service.yaml
+> └── overlays
+>     ├── development
+>     │   ├── cpu_count.yaml
+>     │   ├── kustomization.yaml
+>     │   └── replica_count.yaml
+>     └── production
+>         ├── cpu_count.yaml
+>         ├── kustomization.yaml
+>         └── replica_count.yaml
+> ```
 
-Run `kustomize` on your overlay.  The result
-is printed to `stdout` as a set of complete
-resources, ready to be [applied] to a cluster.
-See the [demos].
+Take the work from step (1) above, move it into a
+`someApp` subdirectory called `base`, then
+place overlays in a sibling directory.
 
+An overlay is just another kustomization, refering to
+the base, and referring to patches to apply to that
+base.
+
+This arrangement makes it easy to manage your
+configuration with `git`.  The base could have files
+from an upstream repository managed by someone else.
+The overlays could be in a repository you own.
+Arranging the repo clones as siblings on disk avoids
+the need for git submodules (though that works fine, if
+you are a submodule fan).
+
+Generate YAML with
+
+```sh
+kustomize build ~/someApp/overlays/production
+```
+
+The YAML can be directly [applied] to a cluster:
+
+> ```sh
+> kustomize build ~/someApp/overlays/production | kubectl apply -f -
+> ```
 
 ## About
 
-This project sponsored by [sig-cli] ([KEP]).
+This tool is sponsored by [sig-cli] ([KEP]).
+
+
+[KEP]: https://github.com/kubernetes/community/blob/master/keps/sig-cli/0008-kustomize.md
+[`make`]: https://www.gnu.org/software/make
+[`sed`]: https://www.gnu.org/software/sed
+[applied]: docs/glossary.md#apply
+[base]: docs/glossary.md#base
+[declarative configuration]: docs/glossary.md#declarative-application-management
+[examples]: examples/README.md
+[imageBase]: docs/base.jpg
+[imageOverlay]: docs/overlay.jpg
+[install]: INSTALL.md
+[kubernetes style]: docs/glossary.md#kubernetes-style-object
+[kustomization]: docs/glossary.md#kustomization
+[overlay]: docs/glossary.md#overlay
+[overlays]: docs/glossary.md#overlay
+[release page]: https://github.com/kubernetes-sigs/kustomize/releases
+[resource]: docs/glossary.md#resource
+[resources]: docs/glossary.md#resource
+[sig-cli]: https://github.com/kubernetes/community/blob/master/sig-cli/README.md
+[variant]: docs/glossary.md#variant
+[variants]: docs/glossary.md#variant
+[workflows]: docs/workflows.md

SECURITY_CONTACTS

@@ -0,0 +1,15 @@
+# Defined below are the security contacts for this repo.
+#
+# They are the contact point for the Product Security Team to reach out
+# to for triaging and handling of incoming issues.
+#
+# The below names agree to abide by the
+# [Embargo Policy](https://github.com/kubernetes/sig-release/blob/master/security-release-process-documentation/security-release-process.md#embargo-policy)
+# and will be removed and replaced if they violate that agreement.
+#
+# DO NOT REPORT SECURITY VULNERABILITIES DIRECTLY TO THESE NAMES, FOLLOW THE
+# INSTRUCTIONS AT https://kubernetes.io/security/
+
+monopole
+Liujingfang1
+pwittrock

bin/pre-commit.sh

@@ -1,4 +1,5 @@
 #!/bin/bash
+set -e
 
 # Make sure, we run in the root of the repo and
 # therefore run the tests on all packages
@@ -31,10 +32,33 @@ function testGoFmt {
   diff <(echo -n) <(go_dirs | xargs -0 gofmt -s -d -l)
 }
 
-function testGoImports {
-  diff -u <(echo -n) <(go_dirs | xargs -0 goimports -l)
+
+function testGoCyclo {
+  diff <(echo -n) <(go_dirs | xargs -0 gocyclo -over 15)
 }
 
+function testGoLint {
+  diff -u <(echo -n) <(go_dirs | xargs -0 golint --min_confidence 0.85 )
+}
+
+function testGoMetalinter {
+  diff -u <(echo -n) <(go_dirs | xargs -0 gometalinter.v2 --disable-all --deadline 5m \
+  --enable=misspell \
+  --enable=structcheck \
+  --enable=deadcode \
+  --enable=goimports \
+  --enable=varcheck \
+  --enable=goconst \
+  --enable=unparam \
+  --enable=ineffassign \
+  --enable=nakedret \
+  --enable=interfacer \
+  --enable=misspell \
+  --line-length=170 --enable=lll \
+  --dupl-threshold=400 --enable=dupl)
+}
+
+
 function testGoVet {
   go vet -all ./...
 }
@@ -43,14 +67,22 @@ function testGoTest {
   go test -v ./...
 }
 
-function testDemos {
-  mdrip --mode test --label test README.md ./demos
+function testExamples {
+  mdrip --mode test --label test README.md ./examples
 }
 
 runTest testGoFmt
-runTest testGoImports
+runTest testGoMetalinter
+runTest testGoLint
 runTest testGoVet
+runTest testGoCyclo
 runTest testGoTest
-runTest testDemos
+runTest testExamples
+
+if [ $rc -eq 0 ]; then
+  echo "SUCCESS!"
+else
+  echo "FAILURE; exit code $rc"
+fi
 
 exit $rc

build/README.md

@@ -1,13 +1,45 @@
-## Overview
+[releases page]: https://github.com/kubernetes-sigs/kustomize/releases
+[`container-builder-local`]: https://github.com/GoogleCloudPlatform/container-builder-local
+[Google Container Builder]: https://cloud.google.com/container-builder
 
-This directory contains scripts and configruation files for publishing a
-`kustomize` release on [release page](https://github.com/kubernetes-sigs/kustomize/releases)
+Scripts and configuration files for publishing a
+`kustomize` release on the [releases page].
 
-## Steps to run build a release locally
-Install container-builder-local from [github](https://github.com/GoogleCloudPlatform/container-builder-local). 
+### Build a release locally
 
-```sh
-container-builder-local --config=build/cloudbuild_local.yaml --dryrun=false --write-workspace=/tmp/w .
+Install [`container-builder-local`], then run
+
+```
+container-builder-local \
+   --config=build/cloudbuild_local.yaml \
+   --dryrun=false --write-workspace=/tmp/w .
 ```
 
-You will find the build artifacts under `/tmp/w/dist` directory
+to build artifacts under `/tmp/w/dist`.
+
+### Publish a Release
+
+Get on an up-to-date master branch:
+```
+git checkout master
+git fetch upstream
+git rebase upstream/master
+```
+
+Define the version (see [semver principles](https://semver.org)), e.g.:
+```
+version=v1.0.3
+```
+
+Tag the repo:
+```
+git tag -a $version -m "$version release"
+```
+
+Push the tag upstream:
+```
+git push upstream $version
+```
+
+The new tag will trigger a job in [Google Container
+Builder] to put a new release on the [releases page].

build/goreleaser.yml

@@ -0,0 +1,33 @@
+# This is an example goreleaser.yaml file with some sane defaults.
+# Make sure to check the documentation at http://goreleaser.com
+project_name: kustomize
+builds:
+- main: ./kustomize.go
+  binary: kustomize
+  ldflags: -s -X github.com/kubernetes-sigs/kustomize/version.kustomizeVersion={{.Version}} -X github.com/kubernetes-sigs/kustomize/version.gitCommit={{.Commit}} -X github.com/kubernetes-sigs/kustomize/version.buildDate={{.Date}}
+  goos:
+  - darwin
+  - linux
+  - windows
+  goarch:
+   - amd64
+  env:
+  - CGO_ENABLED=0
+checksum:
+  name_template: 'checksums.txt'
+archive:
+  format: binary
+snapshot:
+  name_template: "master"
+changelog:
+  sort: asc
+  filters:
+    exclude:
+    - '^docs:'
+    - '^test:'
+    - Merge pull request
+    - Merge branch
+release:
+  github:
+    owner: kubernetes-sigs
+    name: kustomize

docs/glossary.md

@@ -68,25 +68,17 @@ management in k8s.
 
 A _base_ is a [target] that some [overlay] modifies.
 
-Any target, including an overlay, can be a base to
+Any target, including an [overlay], can be a base to
 another target.
 
 A base has no knowledge of the overlays that refer to it.
 
-A base is usable in isolation, i.e. one should
-be able to [apply] a base to a cluster directly.
-
 For simple [gitops] management, a base configuration
 could be the _sole content of a git repository
 dedicated to that purpose_.  Same with [overlays].
 Changes in a repo could generate a build, test and
 deploy cycle.
 
-Some of the demos for [kustomize] will break from this
-idiom and store all demo config files in directories
-_next_ to the `kustomize` code so that the code and
-demos can be more easily maintained by the same group
-of people.
 
 ## bespoke configuration
 
@@ -162,10 +154,10 @@ It's often abbreviated as _k8s_.
 
 An object, expressed in a YAML or JSON file, with the
 [fields required] by kubernetes.  Basically just a
-`kind` field to identify the type, a `metadata/name`
-field to identify the variant, and an `apiVersion`
-field to identify the version (if there's more than one
-version).
+_kind_ field to identify the type, a _metadata/name_
+field to identify the particular instance, and an
+_apiVersion_ field to identify the version (if there's
+more than one version).
 
 ## kustomize
 
@@ -210,19 +202,24 @@ An _overlay_ is a [target] that modifies (and thus
 depends on) another target.
 
 The [kustomization] in an overlay refers to (via file
-path, URI or other method) _some other kustomization_,
+path, URI or other method) some other kustomization,
 known as its [base].
 
 An overlay is unusable without its base.
 
-An overlay supports the typical notion of a
-_development_, _QA_, _staging_ and _production_
-environment variants.
+An overlay may act as a base to another overlay.
 
-The configuration of these environments is specified in
-individual overlays (one per environment) that all
-refer to a common base that holds common configuration.
-One configures the cluster like this:
+Overlays make the most sense when there is _more than
+one_, because they create different [variants] of a
+common base - e.g.  _development_, _QA_, _staging_ and
+_production_ environment variants.
+
+These variants use the same overall resources, and vary
+in relatively simple ways, e.g. the number of replicas
+in a deployment, the CPU to a particular pod, the data
+source used in a configmap, etc.
+
+One configures a cluster like this:
 
 > ```
 >  kustomize build someapp/overlays/staging |\
@@ -232,10 +229,9 @@ One configures the cluster like this:
 >      kubectl apply -f -
 > ```
 
-Usage of the base is implicit (the overlay's kustomization
-points to the base).
+Usage of the base is implicit - the overlay's
+kustomization points to the base.
 
-An overlay may act as a base to another overlay.
 
 ## package
 
@@ -267,7 +263,7 @@ configmap.
 
 More generally, a resource can be any correct YAML file
 that [defines an object](https://kubernetes.io/docs/concepts/overview/working-with-objects/kubernetes-objects/#required-fields)
-with a `kind` and a `metadata/name` field.
+with a _kind_ and a _metadata/name_ field.
 
 
 A _resource_ in the content of a REST-ful API is the
@@ -290,8 +286,7 @@ The _target_ is the argument to `kustomize build`, e.g.:
 > ```
 
 `$target` must be a path to a directory that
-immediately contains a file called
-`kustomization.yaml` (i.e. a [kustomization]).
+immediately contains a [kustomization].
 
 The target contains, or refers to, all the information
 needed to create customized resources to send to the
@@ -304,15 +299,15 @@ A target is a [base] or an [overlay].
 A _variant_ is the outcome, in a cluster, of applying
 an [overlay] to a [base].
 
-> E.g., a _staging_ and _production_ overlay both modify some
-> common base to create distinct variants.
->
-> The _staging_ variant is the set of resources
-> exposed to quality assurance testing, or to some
-> external users who'd like to see what the next
-> version of production will look like.
->
-> The _production_ variant is the set of resources
-> exposed to production traffic, and thus may employ
-> deployments with a large number of replicas and higher
-> cpu and memory requests.
+E.g., a _staging_ and _production_ overlay both modify
+some common base to create distinct variants.
+
+The _staging_ variant is the set of resources exposed
+to quality assurance testing, or to some external users
+who'd like to see what the next version of production
+will look like.
+
+The _production_ variant is the set of resources
+exposed to production traffic, and thus may employ
+deployments with a large number of replicas and higher
+cpu and memory requests.

docs/kustomization.yaml

@@ -32,6 +32,8 @@
 # visible in configuration reviews.
 # ----------------------------------------------------
 
+# Adds namespace to all resources.
+namespace: my-namespace
 
 # Value of this field is prepended to the
 # names of all resources, e.g. a deployment named
@@ -80,6 +82,11 @@ secretGenerator:
     tls.crt: "cat secret/tls.cert"
     tls.key: "cat secret/tls.key"
   type: "kubernetes.io/tls"
+- name: downloaded_secret
+  commands:
+    username: "curl -s https://path/to/secrets/username.yaml"
+    password: "curl -s https://path/to/secrets/password.yaml"
+  type: Opaque
 
 # Each entry in this list should resolve to a directory
 # containing a kustomization file, else the
@@ -113,3 +120,67 @@ patches:
 - service_port_8888.yaml
 - deployment_increase_replicas.yaml
 - deployment_increase_memory.yaml
+
+
+# Each entry in this list should be a relative path to
+# a file for custom resource definition(CRD).
+#
+# The presence of this field is to allow kustomize be
+# aware of CRDs and apply proper
+# transformation for any objects in those types.
+#
+# Typical use case: A CRD object refers to a ConfigMap object.
+# In kustomization, the ConfigMap object name may change by adding namePrefix or hashing
+# The name reference for this ConfigMap object in CRD object need to be
+# updated with namePrefix or hashing in the same way.
+crds:
+- crds/typeA.yaml
+- crds/typeB.yaml
+
+# Vars are used to insert values from resources that cannot be referenced
+# otherwise. For example if you need to pass a Service's name to the arguments
+# or environment variables of a program but without hard coding the actual name
+# of the Service you'd insert `$(MY_SERVICE_NAME)` into the value field of the
+# env var or into the command or args of the container as shown here:
+# ```
+#   containers:
+#     - image: myimage
+#       command: ["start", "--host", "$(MY_SERVICE_NAME)"]
+#       env:
+#         - name: SECRET_TOKEN
+#           value: $(SOME_SECRET_NAME)
+# ```
+#
+# Then you'll add an entry to `vars:` like shown below with the same name
+# and a reference to the resource from which to pull the field's value.
+# The actual field's path is optional and by default it will use
+# `metadata.name`. Currently only string type fields are supported, no integers
+# or booleans, etc. Also array access is currently not possible. For example getting
+# the image field of container number 2 inside of a pod can currently not be done.
+#
+# Not every location of a variable is supported. To see a complete list of locations
+# see the file [refvars.go](https://github.com/kubernetes-sigs/kustomize/blob/master/pkg/transformers/refvars.go#L20).
+#
+# An example of a situation where you'd not use vars is when you'd like to set a
+# pod's `serviceAccountName`. In that case you would just reference the ServiceAccount
+# by name and Kustomize will resolve it to the eventual name while building the manifests.
+vars:
+  - name: SOME_SECRET_NAME
+    objref:
+      kind: Secret
+      name: my-secret
+      apiVersion: v1
+  - name: MY_SERVICE_NAME
+    objref:
+      kind: Service
+      name: my-service
+      apiVersion: v1
+    fieldref:
+      fieldpath: metadata.name
+  - name: ANOTHER_DEPLOYMENTS_POD_RESTART_POLICY
+    objref:
+      kind: Deployment
+      name: my-deployment
+      apiVersion: apps/v1
+    fieldref:
+      fieldpath: spec.template.spec.restartPolicy

docs/workflows.md

@@ -10,7 +10,7 @@
 [patch]: glossary.md#patch
 [patches]: glossary.md#patch
 [rebase]: https://git-scm.com/docs/git-rebase
-[resources]: glossary.md#resources
+[resources]: glossary.md#resource
 [workflowBespoke]: workflowBespoke.jpg
 [workflowOts]: workflowOts.jpg
 
@@ -64,8 +64,8 @@ specified in the base.
 Run kustomize, and pipe the output to [apply].
 
 > ```
-> kustomize ~/ldap/overlays/staging | kubectl apply -f -
-> kustomize ~/ldap/overlays/production | kubectl apply -f -
+> kustomize build ~/ldap/overlays/staging | kubectl apply -f -
+> kustomize build ~/ldap/overlays/production | kubectl apply -f -
 > ```
 
 
@@ -85,13 +85,13 @@ is periodically consulted for updates.
 
 The [base] directory is maintained in a repo whose
 upstream is an [OTS] configuration, in this case
-https://github.com/kinflate/ldap.
+some user's `ldap` repo:
 
 > ```
 > mkdir ~/ldap
 > git clone https://github.com/$USER/ldap ~/ldap/base
 > cd ~/ldap/base
-> git remote add upstream git@github.com:kustomize/ldap
+> git remote add upstream git@github.com:$USER/ldap
 > ```
 
 #### 3) create [overlays]
@@ -107,17 +107,19 @@ The [overlays] are siblings to each other and to the
 > mkdir -p ~/ldap/overlays/production
 > ```
 
+The user can maintain the `overlays` directory in a
+distinct repository.
 
 #### 4) bring up [variants]
 
 > ```
-> kustomize ~/ldap/overlays/staging | kubectl apply -f -
-> kustomize ~/ldap/overlays/production | kubectl apply -f -
+> kustomize build ~/ldap/overlays/staging | kubectl apply -f -
+> kustomize build ~/ldap/overlays/production | kubectl apply -f -
 > ```
 
 #### 5) (optionally) capture changes from upstream
 
-The user can optionally [rebase] their [base] to
+The user can periodically [rebase] their [base] to
 capture changes made in the upstream repository.
 
 > ```

examples/README.md

@@ -1,7 +1,14 @@
-# Demos
+# Examples
 
-These demos assume that `kustomize` is on your `$PATH`.
-They are covered by pre-submit tests.
+These examples assume that `kustomize` is on your `$PATH`.
+
+They are covered by [pre-commit](../bin/pre-commit.sh)
+tests, and should work with HEAD
+
+<!-- @installkustomize @test -->
+```
+go get github.com/kubernetes-sigs/kustomize
+```
 
  * [hello world](helloWorld/README.md) - Deploy multiple
    (differently configured) variants of a simple Hello
@@ -22,3 +29,5 @@ They are covered by pre-submit tests.
 
  * [breakfast](breakfast.md) - Customize breakfast for
    Alice and Bob.
+   
+ * [container args](wordpress/README.md) - Injecting k8s runtime data into container arguments (e.g. to point wordpress to a SQL service).

examples/helloWorld/README.md

@@ -51,7 +51,7 @@ mkdir -p $BASE
 
 curl -s -o "$BASE/#1.yaml" "https://raw.githubusercontent.com\
 /kubernetes-sigs/kustomize\
-/master/demos/helloWorld\
+/master/examples/helloWorld\
 /{configMap,deployment,kustomization,service}.yaml"
 ```
 
@@ -112,6 +112,12 @@ sed -i 's/app: hello/app: my-hello/' \
     $BASE/kustomization.yaml
 ```
 
+On a Mac, use:
+```
+sed -i '' $pattern $file
+```
+to get in-place editing.
+
 See the effect:
 <!-- @checkLabel @test -->
 ```
@@ -397,7 +403,14 @@ the server will use:
 sed -i 's/pineapple/kiwi/' $OVERLAYS/staging/map.yaml
 ```
 
-Run kustomize again to see the new names:
+See the new greeting:
+
+```
+kustomize build $OVERLAYS/staging |\
+  grep -B 2 -A 3 kiwi
+```
+
+Run kustomize again to see the new configMap names:
 
 <!-- @grepStagingName @test -->
 ```
@@ -413,7 +426,8 @@ uses the map:
 <!-- @countHashes @test -->
 ```
 test 3 == \
-  $(kustomize build $OVERLAYS/staging | grep khk45ktkd9 | wc -l)
+  $(kustomize build $OVERLAYS/staging | grep khk45ktkd9 | wc -l); \
+  echo $?
 ```
 
 Applying these resources to the cluster will result in

examples/helloWorld/kustomization.yaml

@@ -5,5 +5,10 @@ commonLabels:
 
 resources:
 - deployment.yaml
-- configMap.yaml
 - service.yaml
+
+configMapGenerator:
+- name: the-map
+  literals:
+    - altGreeting="Good Morning!"
+    - enableRisky="false"

examples/integration_tests.sh

@@ -24,7 +24,7 @@
 #
 # This script assumes that the process running it has
 # checked out the kubernetes-sigs/kustomize repo, and
-# has cd'ed into it (i.e. the directory above "demos")
+# has cd'ed into it (i.e. the directory above "examples")
 # before running it.
 #
 # At time of writing, its 'call point' was in
@@ -79,6 +79,6 @@ function runTest {
 
 setUpEnv
 
-pushd demos
+pushd examples
 runTest ldap/integration_test.sh ldap/base
 popd

examples/ldap/README.md

@@ -45,7 +45,7 @@ mkdir -p $BASE
 
 CONTENT="https://raw.githubusercontent.com\
 /kubernetes-sigs/kustomize\
-/master/demos/ldap"
+/master/examples/ldap"
 
 curl -s -o "$BASE/#1" "$CONTENT/base\
 /{deployment.yaml,kustomization.yaml,service.yaml,env.startup.txt}"

examples/mySql/README.md

@@ -29,7 +29,7 @@ Download them:
 ```
 curl -s  -o "$DEMO_HOME/#1.yaml" "https://raw.githubusercontent.com\
 /kubernetes-sigs/kustomize\
-/master/demos/mySql\
+/master/examples/mySql\
 /{deployment,secret,service}.yaml"
 ```
 

examples/springboot/README.md

@@ -31,7 +31,7 @@ Download them:
 ```
 CONTENT="https://raw.githubusercontent.com\
 /kubernetes-sigs/kustomize\
-/master/demos/springboot"
+/master/examples/springboot"
 
 curl -s -o "$DEMO_HOME/#1.yaml" \
   "$CONTENT/base/{deployment,service}.yaml"

examples/springboot/overlays/production/patch.yaml

@@ -4,7 +4,7 @@ metadata:
   name: demo-configmap
 data:
   application.properties: |
-    app.name=Staging Kinflate Demo
+    app.name=Production Kinflate Demo
     spring.jpa.hibernate.ddl-auto=update
     spring.datasource.url=jdbc:mysql://<production_db_ip>:3306/db_example
     spring.datasource.username=root

examples/wordpress/README.md

@@ -0,0 +1,144 @@
+# Demo: Injecting k8s runtime data into containers
+
+In this tutorial, you will learn how to use `kustomize` to declare a variable reference and substitute it in container's command.
+
+To run WordPress, it's necessary to
+
+- connect WordPress with a MySQL database
+- access the service name of MySQL database from WordPress container
+
+First make a place to work:
+<!-- @makeDemoHome @test -->
+```
+DEMO_HOME=$(mktemp -d)
+MYSQL_HOME=$DEMO_HOME/mysql
+mkdir -p $MYSQL_HOME
+WORDPRESS_HOME=$DEMO_HOME/wordpress
+mkdir -p $WORDPRESS_HOME
+```
+
+### Download resources
+
+Download the resources and `kustomization.yaml` for WordPress.
+
+<!-- @downloadResources @test -->
+```
+CONTENT="https://raw.githubusercontent.com\
+/kubernetes-sigs/kustomize\
+/master/examples/wordpress/wordpress"
+
+curl -s -o "$WORDPRESS_HOME/#1.yaml" \
+  "$CONTENT/{deployment,service,kustomization}.yaml"
+```
+
+Download the resources and `kustomization.yaml` for MySQL.
+
+<!-- @downloadResources @test -->
+```
+CONTENT="https://raw.githubusercontent.com\
+/kubernetes-sigs/kustomize\
+/master/examples/wordpress/mysql"
+
+curl -s -o "$MYSQL_HOME/#1.yaml" \
+  "$CONTENT/{deployment,service,secret,kustomization}.yaml"
+```
+
+### Create kustomization.yaml
+Create a new kustomization with two bases:
+
+<!-- @createKustomization @test -->
+```
+cat <<EOF >$DEMO_HOME/kustomization.yaml
+bases:
+  - wordpress
+  - mysql
+namePrefix: demo-
+EOF
+```
+
+### Download patch for WordPress
+In the new kustomization, apply a patch for wordpress deployment. The patch does two things
+- Add an initial container to show the mysql service name
+- Add environment variable that allow wordpress to find the mysql database
+
+<!-- @downloadPatch @test -->
+```
+CONTENT="https://raw.githubusercontent.com\
+/kubernetes-sigs/kustomize\
+/master/examples/patch.yaml"
+
+curl -s -o "$DEMO_HOME/#1.yaml" \
+  "$CONTENT/{patch}.yaml"
+```
+The patch has following content
+> ```
+> apiVersion: apps/v1beta2
+> kind: Deployment
+> metadata:
+>   name: wordpress
+> spec:
+>   template:
+>     spec:
+>       initContainers:
+>       - name: init-command
+>         image: debian
+>         command:
+>         - "echo $(WORDPRESS_SERVICE)"
+>         - "echo $(MYSQL_SERVICE)"
+>       containers:
+>       - name: wordpress
+>         env:
+>         - name: WORDPRESS_DB_HOST
+>           value: $(MYSQL_SERVICE)
+>         - name: WORDPRESS_DB_PASSWORD
+>           valueFrom:
+>             secretKeyRef:
+>               name: mysql-pass
+>               key: password
+> ```
+The init container's command requires information that depends on k8s resource object fields, represented by the placeholder variables
+$(WORDPRESS_SERVICE) and $(MYSQL_SERVICE).
+
+### Bind the Variables to k8s Object Fields
+
+<!-- @addVarRef @test -->
+```
+cat <<EOF >>$DEMO_HOME/kustomization.yaml
+vars:
+  - name: WORDPRESS_SERVICE
+    objref:
+      kind: Service
+      name: wordpress
+      apiVersion: v1
+    fieldref:
+      fieldpath: metadata.name
+  - name: MYSQL_SERVICE
+    objref:
+      kind: Service
+      name: mysql
+      apiVersion: v1
+EOF
+```
+`WORDPRESS_SERVICE` is from the field `metadata.name` of Service `wordpress`. If we don't specify `fieldref`, the default is `metadata.name`. So `MYSQL_SERVICE` is from the field `metadata.name` of Service `mysql`.
+
+### Substitution
+Confirm the variable substitution:
+
+<!-- @kustomizeBuild @test -->
+```
+kustomize build $DEMO_HOME
+```
+
+Expect this in the output:
+
+> ```
+> (truncated)
+> ...
+>      initContainers:
+>      - command:
+>        - echo demo-wordpress
+>        - echo demo-mysql
+>        image: debian
+>        name: init-command
+>
+> ```

examples/wordpress/kustomization.yaml

@@ -0,0 +1,19 @@
+bases:
+  - wordpress
+  - mysql
+patches:
+  - patch.yaml
+namePrefix: demo-
+
+vars:
+  - name: WORDPRESS_SERVICE
+    objref:
+      kind: Service
+      name: wordpress
+      apiVersion: v1
+  - name: MYSQL_SERVICE
+    objref:
+      kind: Service
+      name: mysql
+      apiVersion: v1
+

examples/wordpress/mysql/deployment.yaml

@@ -0,0 +1,35 @@
+apiVersion: apps/v1beta2 # for versions before 1.9.0 use apps/v1beta2
+kind: Deployment
+metadata:
+  name: mysql
+  labels:
+    app: mysql
+spec:
+  selector:
+    matchLabels:
+      app: mysql
+  strategy:
+    type: Recreate
+  template:
+    metadata:
+      labels:
+        app: mysql
+    spec:
+      containers:
+      - image: mysql:5.6
+        name: mysql
+        env:
+        - name: MYSQL_ROOT_PASSWORD
+          valueFrom:
+            secretKeyRef:
+              name: mysql-pass
+              key: password
+        ports:
+        - containerPort: 3306
+          name: mysql
+        volumeMounts:
+        - name: mysql-persistent-storage
+          mountPath: /var/lib/mysql
+      volumes:
+      - name: mysql-persistent-storage
+        emptyDir: {}

examples/wordpress/mysql/kustomization.yaml

@@ -0,0 +1,4 @@
+resources:
+- deployment.yaml
+- service.yaml
+- secret.yaml

examples/wordpress/mysql/secret.yaml

@@ -0,0 +1,8 @@
+apiVersion: v1
+kind: Secret
+metadata:
+  name: mysql-pass
+type: Opaque
+data:
+  # Default password is "admin".
+  password: YWRtaW4=

examples/wordpress/mysql/service.yaml

@@ -0,0 +1,11 @@
+apiVersion: v1
+kind: Service
+metadata:
+  name: mysql
+  labels:
+    app: mysql
+spec:
+  ports:
+    - port: 3306
+  selector:
+    app: mysql

examples/wordpress/patch.yaml

@@ -0,0 +1,23 @@
+apiVersion: apps/v1beta2
+kind: Deployment
+metadata:
+  name: wordpress
+spec:
+  template:
+    spec:
+      initContainers:
+      - name: init-command
+        image: debian
+        command:
+        - "echo $(WORDPRESS_SERVICE)"
+        - "echo $(MYSQL_SERVICE)"
+      containers:
+      - name: wordpress
+        env:
+        - name: WORDPRESS_DB_HOST
+          value: $(MYSQL_SERVICE)
+        - name: WORDPRESS_DB_PASSWORD
+          valueFrom:
+            secretKeyRef:
+              name: mysql-pass
+              key: password

examples/wordpress/wordpress/deployment.yaml

@@ -0,0 +1,29 @@
+apiVersion: apps/v1beta2 # for versions before 1.9.0 use apps/v1beta2
+kind: Deployment
+metadata:
+  name: wordpress
+  labels:
+    app: wordpress
+spec:
+  selector:
+    matchLabels:
+      app: wordpress
+  strategy:
+    type: Recreate
+  template:
+    metadata:
+      labels:
+        app: wordpress
+    spec:
+      containers:
+      - image: wordpress:4.8-apache
+        name: wordpress
+        ports:
+        - containerPort: 80
+          name: wordpress
+        volumeMounts:
+        - name: wordpress-persistent-storage
+          mountPath: /var/www/html
+      volumes:
+      - name: wordpress-persistent-storage
+        emptyDir: {}

examples/wordpress/wordpress/kustomization.yaml

@@ -0,0 +1,3 @@
+resources:
+- deployment.yaml
+- service.yaml

examples/wordpress/wordpress/service.yaml

@@ -0,0 +1,12 @@
+apiVersion: v1
+kind: Service
+metadata:
+  name: wordpress
+  labels:
+    app: wordpress
+spec:
+  ports:
+    - port: 80
+  selector:
+    app: wordpress
+  type: LoadBalancer

pkg/app/application.go

@@ -14,44 +14,40 @@ See the License for the specific language governing permissions and
 limitations under the License.
 */
 
+// Package app implements state for the set of all resources being customized.
+// Should rename this - there's nothing "app"y about it.
 package app
 
 import (
 	"bytes"
 	"encoding/json"
+	"fmt"
 
 	"github.com/ghodss/yaml"
+	"github.com/golang/glog"
 
 	"github.com/kubernetes-sigs/kustomize/pkg/constants"
+	"github.com/kubernetes-sigs/kustomize/pkg/crds"
 	interror "github.com/kubernetes-sigs/kustomize/pkg/internal/error"
 	"github.com/kubernetes-sigs/kustomize/pkg/loader"
+	"github.com/kubernetes-sigs/kustomize/pkg/resmap"
 	"github.com/kubernetes-sigs/kustomize/pkg/resource"
 	"github.com/kubernetes-sigs/kustomize/pkg/transformers"
 	"github.com/kubernetes-sigs/kustomize/pkg/types"
+	"github.com/pkg/errors"
 )
 
-type Application interface {
-	// Resources computes and returns the resources for the app.
-	Resources() (resource.ResourceCollection, error)
-	// SemiResources computes and returns the resources without name hash and name reference for the app
-	SemiResources() (resource.ResourceCollection, error)
-	// RawResources computes and returns the raw resources from the kustomization file.
-	// It contains resources from
-	// 1) untransformed resources from current kustomization file
-	// 2) transformed resources from sub packages
-	RawResources() (resource.ResourceCollection, error)
-}
-
-var _ Application = &applicationImpl{}
-
-// Private implementation of the Application interface
-type applicationImpl struct {
+// Application implements the guts of the kustomize 'build' command.
+// TODO: Change name, as "application" is overloaded and somewhat
+// misleading (one can customize an RBAC policy).  Perhaps "Target"
+// https://github.com/kubernetes-sigs/kustomize/blob/master/docs/glossary.md#target
+type Application struct {
 	kustomization *types.Kustomization
 	loader        loader.Loader
 }
 
-// NewApp parses the kustomization file at the path using the loader.
-func New(loader loader.Loader) (Application, error) {
+// NewApplication returns a new instance of Application primed with a Loader.
+func NewApplication(loader loader.Loader) (*Application, error) {
 	content, err := loader.Load(constants.KustomizationFileName)
 	if err != nil {
 		return nil, err
@@ -62,186 +58,7 @@ func New(loader loader.Loader) (Application, error) {
 	if err != nil {
 		return nil, err
 	}
-	return &applicationImpl{kustomization: &m, loader: loader}, nil
-}
-
-// Resources computes and returns the resources from the kustomization file.
-// The namehashing for configmap/secrets and resolving name reference is only done
-// in the most top overlay once at the end of getting resources.
-func (a *applicationImpl) Resources() (resource.ResourceCollection, error) {
-	res, err := a.SemiResources()
-	if err != nil {
-		return nil, err
-	}
-	t, err := a.getHashAndReferenceTransformer()
-	if err != nil {
-		return nil, err
-	}
-	err = t.Transform(res)
-	if err != nil {
-		return nil, err
-	}
-	return res, nil
-}
-
-// SemiResources computes and returns the resources without name hash and name reference for the app
-func (a *applicationImpl) SemiResources() (resource.ResourceCollection, error) {
-	errs := &interror.KustomizationErrors{}
-	raw, err := a.rawResources()
-	if err != nil {
-		errs.Append(err)
-	}
-
-	cms, err := resource.NewFromConfigMaps(a.loader, a.kustomization.ConfigMapGenerator)
-	if err != nil {
-		errs.Append(err)
-	}
-	secrets, err := resource.NewFromSecretGenerators(a.loader.Root(), a.kustomization.SecretGenerator)
-	if err != nil {
-		errs.Append(err)
-	}
-	res, err := resource.Merge(cms, secrets)
-	if err != nil {
-		return nil, err
-	}
-
-	allRes, err := resource.MergeWithOverride(raw, res)
-	if err != nil {
-		return nil, err
-	}
-
-	patches, err := resource.NewFromPatches(a.loader, a.kustomization.Patches)
-	if err != nil {
-		errs.Append(err)
-	}
-
-	if len(errs.Get()) > 0 {
-		return nil, errs
-	}
-
-	t, err := a.getTransformer(patches)
-	if err != nil {
-		return nil, err
-	}
-	err = t.Transform(allRes)
-	if err != nil {
-		return nil, err
-	}
-
-	return allRes, nil
-}
-
-// RawResources computes and returns the raw resources from the kustomization file.
-// The namehashing for configmap/secrets and resolving name reference is only done
-// in the most top overlay once at the end of getting resources.
-func (a *applicationImpl) RawResources() (resource.ResourceCollection, error) {
-	res, err := a.rawResources()
-	if err != nil {
-		return nil, err
-	}
-	t, err := a.getHashAndReferenceTransformer()
-	if err != nil {
-		return nil, err
-	}
-	err = t.Transform(res)
-	if err != nil {
-		return nil, err
-	}
-	return res, nil
-}
-
-func (a *applicationImpl) rawResources() (resource.ResourceCollection, error) {
-	subAppResources, errs := a.subAppResources()
-	resources, err := resource.NewFromResources(a.loader, a.kustomization.Resources)
-	if err != nil {
-		errs.Append(err)
-	}
-
-	if len(errs.Get()) > 0 {
-		return nil, errs
-	}
-
-	return resource.Merge(resources, subAppResources)
-}
-
-func (a *applicationImpl) subAppResources() (resource.ResourceCollection, *interror.KustomizationErrors) {
-	sliceOfSubAppResources := []resource.ResourceCollection{}
-	errs := &interror.KustomizationErrors{}
-	for _, pkgPath := range a.kustomization.Bases {
-		subloader, err := a.loader.New(pkgPath)
-		if err != nil {
-			errs.Append(err)
-			continue
-		}
-		subapp, err := New(subloader)
-		if err != nil {
-			errs.Append(err)
-			continue
-		}
-		// Gather all transformed resources from subpackages.
-		subAppResources, err := subapp.SemiResources()
-		if err != nil {
-			errs.Append(err)
-			continue
-		}
-		sliceOfSubAppResources = append(sliceOfSubAppResources, subAppResources)
-	}
-	allResources, err := resource.Merge(sliceOfSubAppResources...)
-	if err != nil {
-		errs.Append(err)
-	}
-	return allResources, errs
-}
-
-// getTransformer generates the following transformers:
-// 1) apply overlay
-// 2) name prefix
-// 3) apply labels
-// 4) apply annotations
-func (a *applicationImpl) getTransformer(patches []*resource.Resource) (transformers.Transformer, error) {
-	ts := []transformers.Transformer{}
-
-	ot, err := transformers.NewOverlayTransformer(patches)
-	if err != nil {
-		return nil, err
-	}
-	ts = append(ts, ot)
-
-	npt, err := transformers.NewDefaultingNamePrefixTransformer(string(a.kustomization.NamePrefix))
-	if err != nil {
-		return nil, err
-	}
-	ts = append(ts, npt)
-
-	lt, err := transformers.NewDefaultingLabelsMapTransformer(a.kustomization.CommonLabels)
-	if err != nil {
-		return nil, err
-	}
-	ts = append(ts, lt)
-
-	at, err := transformers.NewDefaultingAnnotationsMapTransformer(a.kustomization.CommonAnnotations)
-	if err != nil {
-		return nil, err
-	}
-	ts = append(ts, at)
-
-	return transformers.NewMultiTransformer(ts), nil
-}
-
-// getHashAndReferenceTransformer generates the following transformers:
-// 1) name hash for configmap and secrests
-// 2) apply name reference
-func (a *applicationImpl) getHashAndReferenceTransformer() (transformers.Transformer, error) {
-	ts := []transformers.Transformer{}
-	nht := transformers.NewNameHashTransformer()
-	ts = append(ts, nht)
-
-	nrt, err := transformers.NewDefaultingNameReferenceTransformer()
-	if err != nil {
-		return nil, err
-	}
-	ts = append(ts, nrt)
-	return transformers.NewMultiTransformer(ts), nil
+	return &Application{kustomization: &m, loader: loader}, nil
 }
 
 func unmarshal(y []byte, o interface{}) error {
@@ -254,3 +71,249 @@ func unmarshal(y []byte, o interface{}) error {
 	dec.DisallowUnknownFields()
 	return dec.Decode(o)
 }
+
+// MakeCustomizedResMap creates a ResMap per kustomization instructions.
+// The Resources in the returned ResMap are fully customized.
+func (a *Application) MakeCustomizedResMap() (resmap.ResMap, error) {
+	m, err := a.loadCustomizedResMap()
+	if err != nil {
+		return nil, err
+	}
+	return a.resolveRefsToGeneratedResources(m)
+}
+
+// MakeUncustomizedResMap purports to create a ResMap without customization.
+// The Resources in the returned ResMap include all resources mentioned
+// in the kustomization file and transitively reachable via its Bases,
+// and all generated secrets and configMaps.
+// Meant for use in generating a diff against customized resources.
+// TODO: See https://github.com/kubernetes-sigs/kustomize/issues/85
+func (a *Application) MakeUncustomizedResMap() (resmap.ResMap, error) {
+	m, err := a.loadResMapFromBasesAndResources()
+	if err != nil {
+		return nil, err
+	}
+	return a.resolveRefsToGeneratedResources(m)
+}
+
+// resolveRefsToGeneratedResources fixes all name references.
+func (a *Application) resolveRefsToGeneratedResources(m resmap.ResMap) (resmap.ResMap, error) {
+	err := transformers.NewNameHashTransformer().Transform(m)
+	if err != nil {
+		return nil, err
+	}
+
+	r := []transformers.Transformer{}
+	t, err := transformers.NewDefaultingNameReferenceTransformer()
+	if err != nil {
+		return nil, err
+	}
+	r = append(r, t)
+
+	refVars, err := a.resolveRefVars(m)
+	if err != nil {
+		return nil, err
+	}
+	t, err = transformers.NewRefVarTransformer(refVars)
+	if err != nil {
+		return nil, err
+	}
+	r = append(r, t)
+
+	err = transformers.NewMultiTransformer(r).Transform(m)
+	if err != nil {
+		return nil, err
+	}
+	return m, nil
+}
+
+// loadCustomizedResMap loads and customizes resources to build a ResMap.
+func (a *Application) loadCustomizedResMap() (resmap.ResMap, error) {
+	errs := &interror.KustomizationErrors{}
+	result, err := a.loadResMapFromBasesAndResources()
+	if err != nil {
+		errs.Append(errors.Wrap(err, "loadResMapFromBasesAndResources"))
+	}
+	err = crds.RegisterCRDs(a.loader, a.kustomization.CRDs)
+	if err != nil {
+		errs.Append(errors.Wrap(err, "RegisterCRDs"))
+	}
+
+	cms, err := resmap.NewResMapFromConfigMapArgs(a.loader, a.kustomization.ConfigMapGenerator)
+	if err != nil {
+		errs.Append(errors.Wrap(err, "NewResMapFromConfigMapArgs"))
+	}
+	secrets, err := resmap.NewResMapFromSecretArgs(a.loader.Root(), a.kustomization.SecretGenerator)
+	if err != nil {
+		errs.Append(errors.Wrap(err, "NewResMapFromSecretArgs"))
+	}
+	res, err := resmap.MergeWithoutOverride(cms, secrets)
+	if err != nil {
+		return nil, errors.Wrap(err, "Merge")
+	}
+
+	result, err = resmap.MergeWithOverride(result, res)
+	if err != nil {
+		return nil, err
+	}
+
+	patches, err := resmap.NewResourceSliceFromPatches(a.loader, a.kustomization.Patches)
+	if err != nil {
+		errs.Append(errors.Wrap(err, "NewResourceSliceFromPatches"))
+	}
+
+	if len(errs.Get()) > 0 {
+		return nil, errs
+	}
+	t, err := a.newTransformer(patches)
+	if err != nil {
+		return nil, err
+	}
+	err = t.Transform(result)
+	if err != nil {
+		return nil, err
+	}
+	return result, nil
+}
+
+// Gets Bases and Resources as advertised.
+func (a *Application) loadResMapFromBasesAndResources() (resmap.ResMap, error) {
+	bases, errs := a.loadCustomizedBases()
+	resources, err := resmap.NewResMapFromFiles(a.loader, a.kustomization.Resources)
+	if err != nil {
+		errs.Append(errors.Wrap(err, "rawResources failed to read Resources"))
+	}
+	if len(errs.Get()) > 0 {
+		return nil, errs
+	}
+	return resmap.MergeWithoutOverride(resources, bases)
+}
+
+// Loop through the Bases of this kustomization recursively loading resources.
+// Combine into one ResMap, demanding unique Ids for each resource.
+func (a *Application) loadCustomizedBases() (resmap.ResMap, *interror.KustomizationErrors) {
+	list := []resmap.ResMap{}
+	errs := &interror.KustomizationErrors{}
+	for _, path := range a.kustomization.Bases {
+		loader, err := a.loader.New(path)
+		if err != nil {
+			errs.Append(errors.Wrap(err, "couldn't make loader for "+path))
+			continue
+		}
+		app, err := NewApplication(loader)
+		if err != nil {
+			errs.Append(errors.Wrap(err, "couldn't make app for "+path))
+			continue
+		}
+		resMap, err := app.loadCustomizedResMap()
+		if err != nil {
+			errs.Append(errors.Wrap(err, "SemiResources"))
+			continue
+		}
+		list = append(list, resMap)
+	}
+	result, err := resmap.MergeWithoutOverride(list...)
+	if err != nil {
+		errs.Append(errors.Wrap(err, "Merge failed"))
+	}
+	return result, errs
+}
+
+func (a *Application) loadBasesAsFlatList() ([]*Application, error) {
+	var result []*Application
+	errs := &interror.KustomizationErrors{}
+	for _, path := range a.kustomization.Bases {
+		loader, err := a.loader.New(path)
+		if err != nil {
+			errs.Append(err)
+			continue
+		}
+		a, err := NewApplication(loader)
+		if err != nil {
+			errs.Append(err)
+			continue
+		}
+		result = append(result, a)
+	}
+	if len(errs.Get()) > 0 {
+		return nil, errs
+	}
+	return result, nil
+}
+
+// newTransformer makes a Transformer that does everything except resolve generated names.
+func (a *Application) newTransformer(patches []*resource.Resource) (transformers.Transformer, error) {
+	r := []transformers.Transformer{}
+	t, err := transformers.NewPatchTransformer(patches)
+	if err != nil {
+		return nil, err
+	}
+	r = append(r, t)
+	r = append(r, transformers.NewNamespaceTransformer(string(a.kustomization.Namespace)))
+	t, err = transformers.NewDefaultingNamePrefixTransformer(string(a.kustomization.NamePrefix))
+	if err != nil {
+		return nil, err
+	}
+	r = append(r, t)
+	t, err = transformers.NewDefaultingLabelsMapTransformer(a.kustomization.CommonLabels)
+	if err != nil {
+		return nil, err
+	}
+	r = append(r, t)
+	t, err = transformers.NewDefaultingAnnotationsMapTransformer(a.kustomization.CommonAnnotations)
+	if err != nil {
+		return nil, err
+	}
+	r = append(r, t)
+	return transformers.NewMultiTransformer(r), nil
+}
+
+func (a *Application) resolveRefVars(m resmap.ResMap) (map[string]string, error) {
+	result := map[string]string{}
+	vars, err := a.getAllVars()
+	if err != nil {
+		return result, err
+	}
+	for _, v := range vars {
+		id := resource.NewResId(v.ObjRef.GroupVersionKind(), v.ObjRef.Name)
+		if r, found := m[id]; found {
+			s, err := r.GetFieldValue(v.FieldRef.FieldPath)
+			if err != nil {
+				return nil, fmt.Errorf("failed to resolve referred var: %+v", v)
+			}
+			result[v.Name] = s
+		} else {
+			glog.Infof("couldn't resolve v: %v", v)
+		}
+	}
+	return result, nil
+}
+
+// getAllVars returns all the "environment" style Var instances defined in the app.
+func (a *Application) getAllVars() ([]types.Var, error) {
+	result := []types.Var{}
+	errs := &interror.KustomizationErrors{}
+
+	bases, err := a.loadBasesAsFlatList()
+	if err != nil {
+		return nil, err
+	}
+
+	// TODO: computing vars and resources for bases can be combined
+	for _, b := range bases {
+		vars, err := b.getAllVars()
+		if err != nil {
+			errs.Append(err)
+			continue
+		}
+		result = append(result, vars...)
+	}
+	for _, v := range a.kustomization.Vars {
+		v.Defaulting()
+		result = append(result, v)
+	}
+	if len(errs.Get()) > 0 {
+		return nil, errs
+	}
+	return result, nil
+}

pkg/app/application_test.go

@@ -18,29 +18,30 @@ package app
 
 import (
 	"encoding/base64"
-	"fmt"
+	"os"
 	"reflect"
 	"testing"
 
 	"github.com/kubernetes-sigs/kustomize/pkg/constants"
+	"github.com/kubernetes-sigs/kustomize/pkg/internal/loadertest"
 	"github.com/kubernetes-sigs/kustomize/pkg/loader"
-	"github.com/kubernetes-sigs/kustomize/pkg/loader/loadertest"
+	"github.com/kubernetes-sigs/kustomize/pkg/resmap"
 	"github.com/kubernetes-sigs/kustomize/pkg/resource"
-	"github.com/kubernetes-sigs/kustomize/pkg/types"
 	corev1 "k8s.io/api/core/v1"
-	"k8s.io/apimachinery/pkg/apis/meta/v1/unstructured"
 	"k8s.io/apimachinery/pkg/runtime/schema"
 )
 
-func setupTest(t *testing.T) loader.Loader {
-	kustomizationContent := []byte(`
+const (
+	kustomizationContent1 = `
 namePrefix: foo-
+namespace: ns1
 commonLabels:
   app: nginx
 commonAnnotations:
   note: This is a test annotation
 resources:
   - deployment.yaml
+  - namespace.yaml
 configMapGenerator:
 - name: literalConfigMap
   literals:
@@ -52,184 +53,288 @@ secretGenerator:
     DB_USERNAME: "printf admin"
     DB_PASSWORD: "printf somepw"
   type: Opaque
-`)
-	deploymentContent := []byte(`apiVersion: apps/v1
-kind: Deployment
+`
+	deploymentContent = `apiVersion: apps/v1
 metadata:
   name: dply1
-`)
+kind: Deployment
+`
+	namespaceContent = `apiVersion: v1
+kind: Namespace
+metadata:
+  name: ns1
+`
+)
 
+func makeLoader1(t *testing.T) loader.Loader {
 	loader := loadertest.NewFakeLoader("/testpath")
-	err := loader.AddFile("/testpath/"+constants.KustomizationFileName, kustomizationContent)
+	err := loader.AddFile("/testpath/"+constants.KustomizationFileName, []byte(kustomizationContent1))
 	if err != nil {
 		t.Fatalf("Failed to setup fake loader.")
 	}
-	err = loader.AddFile("/testpath/deployment.yaml", deploymentContent)
+	err = loader.AddFile("/testpath/deployment.yaml", []byte(deploymentContent))
+	if err != nil {
+		t.Fatalf("Failed to setup fake loader.")
+	}
+	err = loader.AddFile("/testpath/namespace.yaml", []byte(namespaceContent))
 	if err != nil {
 		t.Fatalf("Failed to setup fake loader.")
 	}
 	return loader
 }
 
-func TestResources(t *testing.T) {
-	expected := resource.ResourceCollection{
-		types.GroupVersionKindName{
-			GVK:  schema.GroupVersionKind{Group: "apps", Version: "v1", Kind: "Deployment"},
-			Name: "dply1",
-		}: &resource.Resource{
-			Data: &unstructured.Unstructured{
-				Object: map[string]interface{}{
-					"apiVersion": "apps/v1",
-					"kind":       "Deployment",
-					"metadata": map[string]interface{}{
-						"name": "foo-dply1",
-						"labels": map[string]interface{}{
+var deploy = schema.GroupVersionKind{Group: "apps", Version: "v1", Kind: "Deployment"}
+var cmap = schema.GroupVersionKind{Version: "v1", Kind: "ConfigMap"}
+var secret = schema.GroupVersionKind{Version: "v1", Kind: "Secret"}
+var ns = schema.GroupVersionKind{Version: "v1", Kind: "Namespace"}
+var svc = schema.GroupVersionKind{Version: "v1", Kind: "Service"}
+
+func TestResources1(t *testing.T) {
+	expected := resmap.ResMap{
+		resource.NewResId(deploy, "dply1"): resource.NewResourceFromMap(
+			map[string]interface{}{
+				"apiVersion": "apps/v1",
+				"kind":       "Deployment",
+				"metadata": map[string]interface{}{
+					"name":      "foo-dply1",
+					"namespace": "ns1",
+					"labels": map[string]interface{}{
+						"app": "nginx",
+					},
+					"annotations": map[string]interface{}{
+						"note": "This is a test annotation",
+					},
+				},
+				"spec": map[string]interface{}{
+					"selector": map[string]interface{}{
+						"matchLabels": map[string]interface{}{
 							"app": "nginx",
 						},
-						"annotations": map[string]interface{}{
-							"note": "This is a test annotation",
-						},
 					},
-					"spec": map[string]interface{}{
-						"selector": map[string]interface{}{
-							"matchLabels": map[string]interface{}{
+					"template": map[string]interface{}{
+						"metadata": map[string]interface{}{
+							"annotations": map[string]interface{}{
+								"note": "This is a test annotation",
+							},
+							"labels": map[string]interface{}{
 								"app": "nginx",
 							},
 						},
-						"template": map[string]interface{}{
-							"metadata": map[string]interface{}{
-								"annotations": map[string]interface{}{
-									"note": "This is a test annotation",
-								},
-								"labels": map[string]interface{}{
-									"app": "nginx",
-								},
+					},
+				},
+			}),
+		resource.NewResId(cmap, "literalConfigMap"): resource.NewResourceFromMap(
+			map[string]interface{}{
+				"apiVersion": "v1",
+				"kind":       "ConfigMap",
+				"metadata": map[string]interface{}{
+					"name":      "foo-literalConfigMap-mc92bgcbh5",
+					"namespace": "ns1",
+					"labels": map[string]interface{}{
+						"app": "nginx",
+					},
+					"annotations": map[string]interface{}{
+						"note": "This is a test annotation",
+					},
+					"creationTimestamp": nil,
+				},
+				"data": map[string]interface{}{
+					"DB_USERNAME": "admin",
+					"DB_PASSWORD": "somepw",
+				},
+			}),
+		resource.NewResId(secret, "secret"): resource.NewResourceFromMap(
+			map[string]interface{}{
+				"apiVersion": "v1",
+				"kind":       "Secret",
+				"metadata": map[string]interface{}{
+					"name":      "foo-secret-877fcfhgt5",
+					"namespace": "ns1",
+					"labels": map[string]interface{}{
+						"app": "nginx",
+					},
+					"annotations": map[string]interface{}{
+						"note": "This is a test annotation",
+					},
+					"creationTimestamp": nil,
+				},
+				"type": string(corev1.SecretTypeOpaque),
+				"data": map[string]interface{}{
+					"DB_USERNAME": base64.StdEncoding.EncodeToString([]byte("admin")),
+					"DB_PASSWORD": base64.StdEncoding.EncodeToString([]byte("somepw")),
+				},
+			}),
+		resource.NewResId(ns, "ns1"): resource.NewResourceFromMap(
+			map[string]interface{}{
+				"apiVersion": "v1",
+				"kind":       "Namespace",
+				"metadata": map[string]interface{}{
+					"name": "foo-ns1",
+					"labels": map[string]interface{}{
+						"app": "nginx",
+					},
+					"annotations": map[string]interface{}{
+						"note": "This is a test annotation",
+					},
+				},
+			}),
+	}
+	l := makeLoader1(t)
+	app, err := NewApplication(l)
+	if err != nil {
+		t.Fatalf("Unexpected construction error %v", err)
+	}
+	actual, err := app.MakeCustomizedResMap()
+	if err != nil {
+		t.Fatalf("Unexpected Resources error %v", err)
+	}
+
+	if !reflect.DeepEqual(actual, expected) {
+		err = expected.ErrorIfNotEqual(actual)
+		t.Fatalf("unexpected inequality: %v", err)
+	}
+}
+
+func TestRawResources1(t *testing.T) {
+	expected := resmap.ResMap{
+		resource.NewResId(deploy, "dply1"): resource.NewResourceFromMap(
+			map[string]interface{}{
+				"apiVersion": "apps/v1",
+				"kind":       "Deployment",
+				"metadata": map[string]interface{}{
+					"name": "dply1",
+				},
+			}),
+		resource.NewResId(ns, "ns1"): resource.NewResourceFromMap(
+			map[string]interface{}{
+				"apiVersion": "v1",
+				"kind":       "Namespace",
+				"metadata": map[string]interface{}{
+					"name": "ns1",
+				},
+			}),
+	}
+	l := makeLoader1(t)
+	app, err := NewApplication(l)
+	if err != nil {
+		t.Fatalf("Unexpected construction error %v", err)
+	}
+	actual, err := app.MakeUncustomizedResMap()
+	if err != nil {
+		t.Fatalf("Unexpected RawResources error %v", err)
+	}
+
+	if err := expected.ErrorIfNotEqual(actual); err != nil {
+		t.Fatalf("unexpected inequality: %v", err)
+	}
+}
+
+const (
+	kustomizationContentBase = `
+namePrefix: foo-
+commonLabels:
+  app: banana
+resources:
+  - deployment.yaml
+`
+	kustomizationContentOverlay = `
+commonLabels:
+  env: staging
+resources:
+  - service.yaml
+bases:
+  - base
+`
+	serviceContent = `apiVersion: v1
+kind: Service
+metadata:
+  name: svc
+spec:
+  type: LoadBalancer
+`
+)
+
+func makeLoader2(t *testing.T) loader.Loader {
+	loader := loadertest.NewFakeLoader("/testpath")
+	err := loader.AddFile("/testpath/"+constants.KustomizationFileName, []byte(kustomizationContentOverlay))
+	if err != nil {
+		t.Fatal(err)
+	}
+	err = loader.AddFile("/testpath/service.yaml", []byte(serviceContent))
+	if err != nil {
+		t.Fatalf("Failed to setup fake loader.")
+	}
+	err = loader.AddDirectory("/testpath/base", os.ModeDir)
+	if err != nil {
+		t.Fatalf("Failed to setup fake loader.")
+	}
+	err = loader.AddFile("/testpath/base/"+constants.KustomizationFileName, []byte(kustomizationContentBase))
+	if err != nil {
+		t.Fatalf("Failed to setup fake loader.")
+	}
+	err = loader.AddFile("/testpath/base/deployment.yaml", []byte(deploymentContent))
+	if err != nil {
+		t.Fatalf("Failed to setup fake loader.")
+	}
+	return loader
+}
+
+// TODO: This test covers incorrect behavior; it should not pass.
+// It asks for raw resources.  The Service resource is returned in raw form,
+// but the resources in the base are modified to have the banana label,
+// the 'foo' name prefix, etc.  This method exists only to support the
+// diff command comparing customized to non-customized resources;
+// perhaps it's not worth supporting the command.
+func TestRawResources2(t *testing.T) {
+	expected := resmap.ResMap{
+		resource.NewResId(deploy, "dply1"): resource.NewResourceFromMap(
+			map[string]interface{}{
+				"apiVersion": "apps/v1",
+				"kind":       "Deployment",
+				"metadata": map[string]interface{}{
+					"name": "foo-dply1",
+					"labels": map[string]interface{}{
+						"app": "banana",
+					},
+				},
+				"spec": map[string]interface{}{
+					"selector": map[string]interface{}{
+						"matchLabels": map[string]interface{}{
+							"app": "banana",
+						},
+					},
+					"template": map[string]interface{}{
+						"metadata": map[string]interface{}{
+							"labels": map[string]interface{}{
+								"app": "banana",
 							},
 						},
 					},
 				},
-			},
-		},
-		types.GroupVersionKindName{
-			GVK:  schema.GroupVersionKind{Version: "v1", Kind: "ConfigMap"},
-			Name: "literalConfigMap",
-		}: &resource.Resource{
-			Data: &unstructured.Unstructured{
-				Object: map[string]interface{}{
-					"apiVersion": "v1",
-					"kind":       "ConfigMap",
-					"metadata": map[string]interface{}{
-						"name": "foo-literalConfigMap-mc92bgcbh5",
-						"labels": map[string]interface{}{
-							"app": "nginx",
-						},
-						"annotations": map[string]interface{}{
-							"note": "This is a test annotation",
-						},
-						"creationTimestamp": nil,
-					},
-					"data": map[string]interface{}{
-						"DB_USERNAME": "admin",
-						"DB_PASSWORD": "somepw",
-					},
+			}),
+		resource.NewResId(svc, "svc"): resource.NewResourceFromMap(
+			map[string]interface{}{
+				"apiVersion": "v1",
+				"kind":       "Service",
+				"metadata": map[string]interface{}{
+					"name": "svc",
 				},
-			},
-		},
-		types.GroupVersionKindName{
-			GVK:  schema.GroupVersionKind{Version: "v1", Kind: "Secret"},
-			Name: "secret",
-		}: &resource.Resource{
-			Data: &unstructured.Unstructured{
-				Object: map[string]interface{}{
-					"apiVersion": "v1",
-					"kind":       "Secret",
-					"metadata": map[string]interface{}{
-						"name": "foo-secret-877fcfhgt5",
-						"labels": map[string]interface{}{
-							"app": "nginx",
-						},
-						"annotations": map[string]interface{}{
-							"note": "This is a test annotation",
-						},
-						"creationTimestamp": nil,
-					},
-					"type": string(corev1.SecretTypeOpaque),
-					"data": map[string]interface{}{
-						"DB_USERNAME": base64.StdEncoding.EncodeToString([]byte("admin")),
-						"DB_PASSWORD": base64.StdEncoding.EncodeToString([]byte("somepw")),
-					},
+				"spec": map[string]interface{}{
+					"type": "LoadBalancer",
 				},
-			},
-		},
+			}),
 	}
-	l := setupTest(t)
-	app, err := New(l)
+	l := makeLoader2(t)
+	app, err := NewApplication(l)
 	if err != nil {
-		t.Fatalf("Unexpected error %v", err)
+		t.Fatalf("Unexpected construction error %v", err)
 	}
-	actual, err := app.Resources()
+	actual, err := app.MakeUncustomizedResMap()
 	if err != nil {
-		t.Fatalf("Unexpected error %v", err)
+		t.Fatalf("Unexpected RawResources error %v", err)
 	}
 
-	if !reflect.DeepEqual(actual, expected) {
-		err = compareMap(actual, expected)
-		t.Fatalf("unexpected error: %v", err)
+	if err := expected.ErrorIfNotEqual(actual); err != nil {
+		t.Fatalf("unexpected inequality: %v", err)
 	}
 }
-
-func TestRawResources(t *testing.T) {
-	expected := resource.ResourceCollection{
-		types.GroupVersionKindName{
-			GVK:  schema.GroupVersionKind{Group: "apps", Version: "v1", Kind: "Deployment"},
-			Name: "dply1",
-		}: &resource.Resource{
-			Data: &unstructured.Unstructured{
-				Object: map[string]interface{}{
-					"apiVersion": "apps/v1",
-					"kind":       "Deployment",
-					"metadata": map[string]interface{}{
-						"name": "dply1",
-					},
-				},
-			},
-		},
-	}
-	l := setupTest(t)
-	app, err := New(l)
-	if err != nil {
-		t.Fatalf("Unexpected error %v", err)
-	}
-	actual, err := app.RawResources()
-	if err != nil {
-		t.Fatalf("Unexpected error %v", err)
-	}
-
-	if err := compareMap(actual, expected); err != nil {
-		t.Fatalf("unexpected error: %v", err)
-	}
-}
-
-func compareMap(m1, m2 resource.ResourceCollection) error {
-	if len(m1) != len(m2) {
-		keySet1 := []types.GroupVersionKindName{}
-		keySet2 := []types.GroupVersionKindName{}
-		for GVKn := range m1 {
-			keySet1 = append(keySet1, GVKn)
-		}
-		for GVKn := range m1 {
-			keySet2 = append(keySet2, GVKn)
-		}
-		return fmt.Errorf("maps has different number of entries: %#v doesn't equals %#v", keySet1, keySet2)
-	}
-	for GVKn, obj1 := range m1 {
-		obj2, found := m2[GVKn]
-		if !found {
-			return fmt.Errorf("%#v doesn't exist in %#v", GVKn, m2)
-		}
-		if !reflect.DeepEqual(obj1, obj2) {
-			return fmt.Errorf("%#v doesn't match %#v", obj1, obj2)
-		}
-	}
-	return nil
-}

pkg/commands/addbase.go

@@ -0,0 +1,99 @@
+/*
+Copyright 2018 The Kubernetes Authors.
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+*/
+
+package commands
+
+import (
+	"errors"
+	"fmt"
+	"strings"
+
+	"github.com/spf13/cobra"
+
+	"github.com/kubernetes-sigs/kustomize/pkg/constants"
+	"github.com/kubernetes-sigs/kustomize/pkg/fs"
+)
+
+type addBaseOptions struct {
+	baseDirectoryPaths string
+}
+
+// newCmdAddBase adds the file path of the kustomize base to the kustomization file.
+func newCmdAddBase(fsys fs.FileSystem) *cobra.Command {
+	var o addBaseOptions
+
+	cmd := &cobra.Command{
+		Use:   "base",
+		Short: "Adds one or more bases to the kustomization.yaml in current directory",
+		Example: `
+		add base {filepath1},{filepath2}`,
+		RunE: func(cmd *cobra.Command, args []string) error {
+			err := o.Validate(args)
+			if err != nil {
+				return err
+			}
+			err = o.Complete(cmd, args)
+			if err != nil {
+				return err
+			}
+			return o.RunAddBase(fsys)
+		},
+	}
+	return cmd
+}
+
+// Validate validates addBase command.
+func (o *addBaseOptions) Validate(args []string) error {
+	if len(args) != 1 {
+		return errors.New("must specify a base directory")
+	}
+	o.baseDirectoryPaths = args[0]
+	return nil
+}
+
+// Complete completes addBase command.
+func (o *addBaseOptions) Complete(cmd *cobra.Command, args []string) error {
+	return nil
+}
+
+// RunAddBase runs addBase command (do real work).
+func (o *addBaseOptions) RunAddBase(fsys fs.FileSystem) error {
+	mf, err := newKustomizationFile(constants.KustomizationFileName, fsys)
+	if err != nil {
+		return err
+	}
+
+	m, err := mf.read()
+	if err != nil {
+		return err
+	}
+
+	// split directory paths
+	paths := strings.Split(o.baseDirectoryPaths, ",")
+	for _, path := range paths {
+		_, err := fsys.Stat(path)
+		if err != nil {
+			return err
+		}
+		if stringInSlice(path, m.Bases) {
+			return fmt.Errorf("base %s already in kustomization file", path)
+		}
+		m.Bases = append(m.Bases, path)
+
+	}
+
+	return mf.write(m)
+}

pkg/commands/addbase_test.go

@@ -0,0 +1,100 @@
+/*
+Copyright 2018 The Kubernetes Authors.
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+*/
+
+package commands
+
+import (
+	"testing"
+
+	"strings"
+
+	"github.com/kubernetes-sigs/kustomize/pkg/constants"
+	"github.com/kubernetes-sigs/kustomize/pkg/fs"
+)
+
+const (
+	baseDirectoryPaths = "my/path/to/wonderful/base,other/path/to/even/more/wonderful/base"
+)
+
+func TestAddBaseHappyPath(t *testing.T) {
+	fakeFS := fs.MakeFakeFS()
+	bases := strings.Split(baseDirectoryPaths, ",")
+	for _, base := range bases {
+		fakeFS.Mkdir(base, 0777)
+	}
+	fakeFS.WriteFile(constants.KustomizationFileName, []byte(kustomizationContent))
+
+	cmd := newCmdAddBase(fakeFS)
+	args := []string{baseDirectoryPaths}
+	err := cmd.RunE(cmd, args)
+	if err != nil {
+		t.Errorf("unexpected cmd error: %v", err)
+	}
+	content, err := fakeFS.ReadFile(constants.KustomizationFileName)
+	if err != nil {
+		t.Errorf("unexpected read error: %v", err)
+	}
+
+	for _, base := range bases {
+		if !strings.Contains(string(content), base) {
+			t.Errorf("expected base name in kustomization")
+		}
+	}
+}
+
+func TestAddBaseAlreadyThere(t *testing.T) {
+	fakeFS := fs.MakeFakeFS()
+	// Create fake directories
+	bases := strings.Split(baseDirectoryPaths, ",")
+	for _, base := range bases {
+		fakeFS.Mkdir(base, 0777)
+	}
+	fakeFS.WriteFile(constants.KustomizationFileName, []byte(kustomizationContent))
+
+	cmd := newCmdAddBase(fakeFS)
+	args := []string{baseDirectoryPaths}
+	err := cmd.RunE(cmd, args)
+	if err != nil {
+		t.Fatalf("unexpected cmd error: %v", err)
+	}
+	// adding an existing base should return an error
+	err = cmd.RunE(cmd, args)
+	if err == nil {
+		t.Errorf("expected already there problem")
+	}
+	var expectedErrors []string
+	for _, base := range bases {
+		error := "base " + base + " already in kustomization file"
+		expectedErrors = append(expectedErrors, error)
+		if !stringInSlice(error, expectedErrors) {
+			t.Errorf("unexpected error %v", err)
+		}
+	}
+
+}
+
+func TestAddBaseNoArgs(t *testing.T) {
+	fakeFS := fs.MakeFakeFS()
+
+	cmd := newCmdAddBase(fakeFS)
+	err := cmd.Execute()
+	if err == nil {
+		t.Errorf("expected error: %v", err)
+	}
+	if err.Error() != "must specify a base directory" {
+		t.Errorf("incorrect error: %v", err.Error())
+	}
+}

pkg/commands/addpatch.go

@@ -19,12 +19,11 @@ package commands
 import (
 	"errors"
 	"fmt"
-	"io"
 
 	"github.com/spf13/cobra"
 
 	"github.com/kubernetes-sigs/kustomize/pkg/constants"
-	"github.com/kubernetes-sigs/kustomize/pkg/util/fs"
+	"github.com/kubernetes-sigs/kustomize/pkg/fs"
 )
 
 type addPatchOptions struct {
@@ -32,7 +31,7 @@ type addPatchOptions struct {
 }
 
 // newCmdAddPatch adds the name of a file containing a patch to the kustomization file.
-func newCmdAddPatch(out, errOut io.Writer, fsys fs.FileSystem) *cobra.Command {
+func newCmdAddPatch(fsys fs.FileSystem) *cobra.Command {
 	var o addPatchOptions
 
 	cmd := &cobra.Command{
@@ -49,7 +48,7 @@ func newCmdAddPatch(out, errOut io.Writer, fsys fs.FileSystem) *cobra.Command {
 			if err != nil {
 				return err
 			}
-			return o.RunAddPatch(out, errOut, fsys)
+			return o.RunAddPatch(fsys)
 		},
 	}
 	return cmd
@@ -70,7 +69,7 @@ func (o *addPatchOptions) Complete(cmd *cobra.Command, args []string) error {
 }
 
 // RunAddPatch runs addPatch command (do real work).
-func (o *addPatchOptions) RunAddPatch(out, errOut io.Writer, fsys fs.FileSystem) error {
+func (o *addPatchOptions) RunAddPatch(fsys fs.FileSystem) error {
 	_, err := fsys.Stat(o.patchFilePath)
 	if err != nil {
 		return err

pkg/commands/addpatch_test.go

@@ -17,14 +17,12 @@ limitations under the License.
 package commands
 
 import (
-	"bytes"
-	"os"
 	"testing"
 
 	"strings"
 
 	"github.com/kubernetes-sigs/kustomize/pkg/constants"
-	"github.com/kubernetes-sigs/kustomize/pkg/util/fs"
+	"github.com/kubernetes-sigs/kustomize/pkg/fs"
 )
 
 const (
@@ -36,12 +34,11 @@ sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.
 )
 
 func TestAddPatchHappyPath(t *testing.T) {
-	buf := bytes.NewBuffer([]byte{})
 	fakeFS := fs.MakeFakeFS()
 	fakeFS.WriteFile(patchFileName, []byte(patchFileContent))
 	fakeFS.WriteFile(constants.KustomizationFileName, []byte(kustomizationContent))
 
-	cmd := newCmdAddPatch(buf, os.Stderr, fakeFS)
+	cmd := newCmdAddPatch(fakeFS)
 	args := []string{patchFileName}
 	err := cmd.RunE(cmd, args)
 	if err != nil {
@@ -57,12 +54,11 @@ func TestAddPatchHappyPath(t *testing.T) {
 }
 
 func TestAddPatchAlreadyThere(t *testing.T) {
-	buf := bytes.NewBuffer([]byte{})
 	fakeFS := fs.MakeFakeFS()
 	fakeFS.WriteFile(patchFileName, []byte(patchFileContent))
 	fakeFS.WriteFile(constants.KustomizationFileName, []byte(kustomizationContent))
 
-	cmd := newCmdAddPatch(buf, os.Stderr, fakeFS)
+	cmd := newCmdAddPatch(fakeFS)
 	args := []string{patchFileName}
 	err := cmd.RunE(cmd, args)
 	if err != nil {
@@ -80,10 +76,9 @@ func TestAddPatchAlreadyThere(t *testing.T) {
 }
 
 func TestAddPatchNoArgs(t *testing.T) {
-	buf := bytes.NewBuffer([]byte{})
 	fakeFS := fs.MakeFakeFS()
 
-	cmd := newCmdAddPatch(buf, os.Stderr, fakeFS)
+	cmd := newCmdAddPatch(fakeFS)
 	err := cmd.Execute()
 	if err == nil {
 		t.Errorf("expected error: %v", err)

pkg/commands/addresource.go

@@ -19,12 +19,11 @@ package commands
 import (
 	"errors"
 	"fmt"
-	"io"
 
 	"github.com/spf13/cobra"
 
 	"github.com/kubernetes-sigs/kustomize/pkg/constants"
-	"github.com/kubernetes-sigs/kustomize/pkg/util/fs"
+	"github.com/kubernetes-sigs/kustomize/pkg/fs"
 )
 
 type addResourceOptions struct {
@@ -32,7 +31,7 @@ type addResourceOptions struct {
 }
 
 // newCmdAddResource adds the name of a file containing a resource to the kustomization file.
-func newCmdAddResource(out, errOut io.Writer, fsys fs.FileSystem) *cobra.Command {
+func newCmdAddResource(fsys fs.FileSystem) *cobra.Command {
 	var o addResourceOptions
 
 	cmd := &cobra.Command{
@@ -49,7 +48,7 @@ func newCmdAddResource(out, errOut io.Writer, fsys fs.FileSystem) *cobra.Command
 			if err != nil {
 				return err
 			}
-			return o.RunAddResource(out, errOut, fsys)
+			return o.RunAddResource(fsys)
 		},
 	}
 	return cmd
@@ -70,7 +69,7 @@ func (o *addResourceOptions) Complete(cmd *cobra.Command, args []string) error {
 }
 
 // RunAddResource runs addResource command (do real work).
-func (o *addResourceOptions) RunAddResource(out, errOut io.Writer, fsys fs.FileSystem) error {
+func (o *addResourceOptions) RunAddResource(fsys fs.FileSystem) error {
 	_, err := fsys.Stat(o.resourceFilePath)
 	if err != nil {
 		return err

pkg/commands/addresource_test.go

@@ -17,14 +17,12 @@ limitations under the License.
 package commands
 
 import (
-	"bytes"
-	"os"
 	"testing"
 
 	"strings"
 
 	"github.com/kubernetes-sigs/kustomize/pkg/constants"
-	"github.com/kubernetes-sigs/kustomize/pkg/util/fs"
+	"github.com/kubernetes-sigs/kustomize/pkg/fs"
 )
 
 const (
@@ -52,12 +50,11 @@ secretGenerator: []
 )
 
 func TestAddResourceHappyPath(t *testing.T) {
-	buf := bytes.NewBuffer([]byte{})
 	fakeFS := fs.MakeFakeFS()
 	fakeFS.WriteFile(resourceFileName, []byte(resourceFileContent))
 	fakeFS.WriteFile(constants.KustomizationFileName, []byte(kustomizationContent))
 
-	cmd := newCmdAddResource(buf, os.Stderr, fakeFS)
+	cmd := newCmdAddResource(fakeFS)
 	args := []string{resourceFileName}
 	err := cmd.RunE(cmd, args)
 	if err != nil {
@@ -73,12 +70,11 @@ func TestAddResourceHappyPath(t *testing.T) {
 }
 
 func TestAddResourceAlreadyThere(t *testing.T) {
-	buf := bytes.NewBuffer([]byte{})
 	fakeFS := fs.MakeFakeFS()
 	fakeFS.WriteFile(resourceFileName, []byte(resourceFileContent))
 	fakeFS.WriteFile(constants.KustomizationFileName, []byte(kustomizationContent))
 
-	cmd := newCmdAddResource(buf, os.Stderr, fakeFS)
+	cmd := newCmdAddResource(fakeFS)
 	args := []string{resourceFileName}
 	err := cmd.RunE(cmd, args)
 	if err != nil {
@@ -96,10 +92,9 @@ func TestAddResourceAlreadyThere(t *testing.T) {
 }
 
 func TestAddResourceNoArgs(t *testing.T) {
-	buf := bytes.NewBuffer([]byte{})
 	fakeFS := fs.MakeFakeFS()
 
-	cmd := newCmdAddResource(buf, os.Stderr, fakeFS)
+	cmd := newCmdAddResource(fakeFS)
 	err := cmd.Execute()
 	if err == nil {
 		t.Errorf("expected error: %v", err)

pkg/commands/build.go

@@ -26,9 +26,8 @@ import (
 
 	"github.com/kubernetes-sigs/kustomize/pkg/app"
 	"github.com/kubernetes-sigs/kustomize/pkg/constants"
+	"github.com/kubernetes-sigs/kustomize/pkg/fs"
 	"github.com/kubernetes-sigs/kustomize/pkg/loader"
-	kutil "github.com/kubernetes-sigs/kustomize/pkg/util"
-	"github.com/kubernetes-sigs/kustomize/pkg/util/fs"
 )
 
 type buildOptions struct {
@@ -36,7 +35,7 @@ type buildOptions struct {
 }
 
 // newCmdBuild creates a new build command.
-func newCmdBuild(out, errOut io.Writer, fs fs.FileSystem) *cobra.Command {
+func newCmdBuild(out io.Writer, fs fs.FileSystem) *cobra.Command {
 	var o buildOptions
 
 	cmd := &cobra.Command{
@@ -44,12 +43,13 @@ func newCmdBuild(out, errOut io.Writer, fs fs.FileSystem) *cobra.Command {
 		Short: "Print current configuration per contents of " + constants.KustomizationFileName,
 		Example: "Use the file somedir/" + constants.KustomizationFileName +
 			" to generate a set of api resources:\nbuild somedir/",
+		SilenceUsage: true,
 		RunE: func(cmd *cobra.Command, args []string) error {
 			err := o.Validate(args)
 			if err != nil {
 				return err
 			}
-			return o.RunBuild(out, errOut, fs)
+			return o.RunBuild(out, fs)
 		},
 	}
 	return cmd
@@ -69,7 +69,7 @@ func (o *buildOptions) Validate(args []string) error {
 }
 
 // RunBuild runs build command.
-func (o *buildOptions) RunBuild(out, errOut io.Writer, fs fs.FileSystem) error {
+func (o *buildOptions) RunBuild(out io.Writer, fs fs.FileSystem) error {
 	l := loader.Init([]loader.SchemeLoader{loader.NewFileLoader(fs)})
 
 	absPath, err := filepath.Abs(o.kustomizationPath)
@@ -82,19 +82,19 @@ func (o *buildOptions) RunBuild(out, errOut io.Writer, fs fs.FileSystem) error {
 		return err
 	}
 
-	application, err := app.New(rootLoader)
+	application, err := app.NewApplication(rootLoader)
 	if err != nil {
 		return err
 	}
 
-	allResources, err := application.Resources()
+	allResources, err := application.MakeCustomizedResMap()
 
 	if err != nil {
 		return err
 	}
 
 	// Output the objects.
-	res, err := kutil.Encode(allResources)
+	res, err := allResources.EncodeAsYaml()
 	if err != nil {
 		return err
 	}

pkg/commands/build_test.go

@@ -28,7 +28,7 @@ import (
 	"github.com/ghodss/yaml"
 
 	"github.com/kubernetes-sigs/kustomize/pkg/constants"
-	"github.com/kubernetes-sigs/kustomize/pkg/util/fs"
+	"github.com/kubernetes-sigs/kustomize/pkg/fs"
 	"k8s.io/apimachinery/pkg/util/sets"
 )
 
@@ -104,49 +104,51 @@ func TestBuild(t *testing.T) {
 	}
 
 	for _, testcaseName := range testcases.List() {
-		t.Run(testcaseName, func(t *testing.T) {
-			name := testcaseName
-			testcase := buildTestCase{}
-			testcaseDir := filepath.Join("testdata", "testcase-"+name)
-			testcaseData, err := ioutil.ReadFile(filepath.Join(testcaseDir, "test.yaml"))
-			if err != nil {
-				t.Fatalf("%s: %v", name, err)
-			}
-			if err := yaml.Unmarshal(testcaseData, &testcase); err != nil {
-				t.Fatalf("%s: %v", name, err)
-			}
-
-			ops := &buildOptions{
-				kustomizationPath: testcase.Filename,
-			}
-			buf := bytes.NewBuffer([]byte{})
-			err = ops.RunBuild(buf, os.Stderr, fs)
-			switch {
-			case err != nil && len(testcase.ExpectedError) == 0:
-				t.Errorf("unexpected error: %v", err)
-			case err != nil && len(testcase.ExpectedError) != 0:
-				if !strings.Contains(err.Error(), testcase.ExpectedError) {
-					t.Errorf("expected error to contain %q but got: %v", testcase.ExpectedError, err)
-				}
-				return
-			case err == nil && len(testcase.ExpectedError) != 0:
-				t.Errorf("unexpected no error")
-			}
-
-			actualBytes := buf.Bytes()
-			if !updateKustomizeExpected {
-				expectedBytes, err := ioutil.ReadFile(testcase.ExpectedStdout)
-				if err != nil {
-					t.Errorf("unexpected error: %v", err)
-				}
-				if !reflect.DeepEqual(actualBytes, expectedBytes) {
-					t.Errorf("%s\ndoesn't equal expected:\n%s\n", actualBytes, expectedBytes)
-				}
-			} else {
-				ioutil.WriteFile(testcase.ExpectedStdout, actualBytes, 0644)
-			}
-
-		})
+		t.Run(testcaseName, func(t *testing.T) { runBuildTestCase(t, testcaseName, updateKustomizeExpected, fs) })
+	}
+
+}
+
+func runBuildTestCase(t *testing.T, testcaseName string, updateKustomizeExpected bool, fs fs.FileSystem) {
+	name := testcaseName
+	testcase := buildTestCase{}
+	testcaseDir := filepath.Join("testdata", "testcase-"+name)
+	testcaseData, err := ioutil.ReadFile(filepath.Join(testcaseDir, "test.yaml"))
+	if err != nil {
+		t.Fatalf("%s: %v", name, err)
+	}
+	if err := yaml.Unmarshal(testcaseData, &testcase); err != nil {
+		t.Fatalf("%s: %v", name, err)
+	}
+
+	ops := &buildOptions{
+		kustomizationPath: testcase.Filename,
+	}
+	buf := bytes.NewBuffer([]byte{})
+	err = ops.RunBuild(buf, fs)
+	switch {
+	case err != nil && len(testcase.ExpectedError) == 0:
+		t.Errorf("unexpected error: %v", err)
+	case err != nil && len(testcase.ExpectedError) != 0:
+		if !strings.Contains(err.Error(), testcase.ExpectedError) {
+			t.Errorf("expected error to contain %q but got: %v", testcase.ExpectedError, err)
+		}
+		return
+	case err == nil && len(testcase.ExpectedError) != 0:
+		t.Errorf("unexpected no error")
+	}
+
+	actualBytes := buf.Bytes()
+	if !updateKustomizeExpected {
+		expectedBytes, err := ioutil.ReadFile(testcase.ExpectedStdout)
+		if err != nil {
+			t.Errorf("unexpected error: %v", err)
+		}
+		if !reflect.DeepEqual(actualBytes, expectedBytes) {
+			t.Errorf("%s\ndoesn't equal expected:\n%s\n", actualBytes, expectedBytes)
+		}
+	} else {
+		ioutil.WriteFile(testcase.ExpectedStdout, actualBytes, 0644)
 	}
 
 }

pkg/commands/commands.go

@@ -14,15 +14,14 @@ See the License for the specific language governing permissions and
 limitations under the License.
 */
 
+// Package commands holds the CLI glue mapping textual commands/args to method calls.
 package commands
 
 import (
 	"flag"
-	"io"
 	"os"
 
-	"github.com/kubernetes-sigs/kustomize/pkg/util/fs"
-	"github.com/kubernetes-sigs/kustomize/version"
+	"github.com/kubernetes-sigs/kustomize/pkg/fs"
 	"github.com/spf13/cobra"
 )
 
@@ -37,15 +36,16 @@ func NewDefaultCommand() *cobra.Command {
 		Long: `
 kustomize manages declarative configuration of Kubernetes.
 
-More info at https://github.com/kubernetes/kubectl/tree/master/cmd/kustomize
+See https://github.com/kubernetes-sigs/kustomize
 `,
 	}
 
 	c.AddCommand(
-		newCmdBuild(stdOut, stdErr, fsys),
+		// TODO: Make consistent API for newCmd* functions.
+		newCmdBuild(stdOut, fsys),
 		newCmdDiff(stdOut, stdErr, fsys),
-		newCmdEdit(stdOut, stdErr, fsys),
-		version.NewCmdVersion(stdOut),
+		newCmdEdit(fsys),
+		newCmdVersion(stdOut),
 	)
 	c.PersistentFlags().AddGoFlagSet(flag.CommandLine)
 
@@ -56,7 +56,7 @@ More info at https://github.com/kubernetes/kubectl/tree/master/cmd/kustomize
 }
 
 // newCmdEdit returns an instance of 'edit' subcommand.
-func newCmdEdit(stdOut, stdErr io.Writer, fsys fs.FileSystem) *cobra.Command {
+func newCmdEdit(fsys fs.FileSystem) *cobra.Command {
 	c := &cobra.Command{
 		Use:   "edit",
 		Short: "Edits a kustomization file",
@@ -71,43 +71,45 @@ func newCmdEdit(stdOut, stdErr io.Writer, fsys fs.FileSystem) *cobra.Command {
 		Args: cobra.MinimumNArgs(1),
 	}
 	c.AddCommand(
-		newCmdAdd(stdOut, stdErr, fsys),
-		newCmdSet(stdOut, stdErr, fsys),
+		newCmdAdd(fsys),
+		newCmdSet(fsys),
 	)
 	return c
 }
 
 // newAddCommand returns an instance of 'add' subcommand.
-func newCmdAdd(stdOut, stdErr io.Writer, fsys fs.FileSystem) *cobra.Command {
+func newCmdAdd(fsys fs.FileSystem) *cobra.Command {
 	c := &cobra.Command{
 		Use:   "add",
-		Short: "Adds configmap/resource/secret to the kustomization file.",
+		Short: "Adds configmap/resource/patch/base to the kustomization file.",
 		Long:  "",
 		Example: `
 	# Adds a configmap to the kustomization file
 	kustomize edit add configmap NAME --from-literal=k=v
 
-	# Adds a secret to the kustomization file
-	kustomize edit add secret NAME --from-literal=k=v
-
 	# Adds a resource to the kustomization
 	kustomize edit add resource <filepath>
 
 	# Adds a patch to the kustomization
 	kustomize edit add patch <filepath>
+
+	# Adds one or more base directories to the kustomization
+	kustomize edit add base <filepath>
+	kustomize edit add base <filepath1>,<filepath2>,<filepath3>
 `,
 		Args: cobra.MinimumNArgs(1),
 	}
 	c.AddCommand(
-		newCmdAddResource(stdOut, stdErr, fsys),
-		newCmdAddPatch(stdOut, stdErr, fsys),
-		newCmdAddConfigMap(stdErr, fsys),
+		newCmdAddResource(fsys),
+		newCmdAddPatch(fsys),
+		newCmdAddConfigMap(fsys),
+		newCmdAddBase(fsys),
 	)
 	return c
 }
 
 // newSetCommand returns an instance of 'set' subcommand.
-func newCmdSet(stdOut, stdErr io.Writer, fsys fs.FileSystem) *cobra.Command {
+func newCmdSet(fsys fs.FileSystem) *cobra.Command {
 	c := &cobra.Command{
 		Use:   "set",
 		Short: "Sets the value of different fields in kustomization file.",
@@ -120,7 +122,7 @@ func newCmdSet(stdOut, stdErr io.Writer, fsys fs.FileSystem) *cobra.Command {
 	}
 
 	c.AddCommand(
-		newCmdSetNamePrefix(stdOut, stdErr, fsys),
+		newCmdSetNamePrefix(fsys),
 	)
 	return c
 }

pkg/commands/configmap.go

@@ -18,17 +18,16 @@ package commands
 
 import (
 	"fmt"
-	"io"
 
 	"github.com/spf13/cobra"
 
 	"github.com/kubernetes-sigs/kustomize/pkg/configmapandsecret"
 	"github.com/kubernetes-sigs/kustomize/pkg/constants"
+	"github.com/kubernetes-sigs/kustomize/pkg/fs"
 	"github.com/kubernetes-sigs/kustomize/pkg/types"
-	"github.com/kubernetes-sigs/kustomize/pkg/util/fs"
 )
 
-func newCmdAddConfigMap(errOut io.Writer, fsys fs.FileSystem) *cobra.Command {
+func newCmdAddConfigMap(fsys fs.FileSystem) *cobra.Command {
 	var config dataConfig
 	cmd := &cobra.Command{
 		Use:   "configmap NAME [--from-file=[key=]source] [--from-literal=key1=value1]",
@@ -76,7 +75,9 @@ func newCmdAddConfigMap(errOut io.Writer, fsys fs.FileSystem) *cobra.Command {
 		&config.FileSources,
 		"from-file",
 		[]string{},
-		"Key file can be specified using its file path, in which case file basename will be used as configmap key, or optionally with a key and file path, in which case the given key will be used.  Specifying a directory will iterate each named file in the directory whose basename is a valid configmap key.")
+		"Key file can be specified using its file path, in which case file basename will be used as configmap "+
+			"key, or optionally with a key and file path, in which case the given key will be used.  Specifying a "+
+			"directory will iterate each named file in the directory whose basename is a valid configmap key.")
 	cmd.Flags().StringArrayVar(
 		&config.LiteralSources,
 		"from-literal",

pkg/commands/configmap_test.go

@@ -19,12 +19,12 @@ package commands
 import (
 	"testing"
 
+	"github.com/kubernetes-sigs/kustomize/pkg/fs"
 	"github.com/kubernetes-sigs/kustomize/pkg/types"
-	"github.com/kubernetes-sigs/kustomize/pkg/util/fs"
 )
 
 func TestNewAddConfigMapIsNotNil(t *testing.T) {
-	if newCmdAddConfigMap(nil, fs.MakeFakeFS()) == nil {
+	if newCmdAddConfigMap(fs.MakeFakeFS()) == nil {
 		t.Fatal("newCmdAddConfigMap shouldn't be nil")
 	}
 }

pkg/commands/diff.go

@@ -25,10 +25,9 @@ import (
 
 	"github.com/kubernetes-sigs/kustomize/pkg/app"
 	"github.com/kubernetes-sigs/kustomize/pkg/constants"
+	"github.com/kubernetes-sigs/kustomize/pkg/diff"
+	"github.com/kubernetes-sigs/kustomize/pkg/fs"
 	"github.com/kubernetes-sigs/kustomize/pkg/loader"
-	"github.com/kubernetes-sigs/kustomize/pkg/util"
-	"github.com/kubernetes-sigs/kustomize/pkg/util/fs"
-	"k8s.io/utils/exec"
 )
 
 type diffOptions struct {
@@ -43,7 +42,7 @@ func newCmdDiff(out, errOut io.Writer, fs fs.FileSystem) *cobra.Command {
 		Use:   "diff [path]",
 		Short: "diff between customized resources and uncustomized resources",
 		RunE: func(cmd *cobra.Command, args []string) error {
-			err := o.Validate(cmd, args)
+			err := o.Validate(args)
 			if err != nil {
 				return err
 			}
@@ -54,7 +53,7 @@ func newCmdDiff(out, errOut io.Writer, fs fs.FileSystem) *cobra.Command {
 }
 
 // Validate validates diff command.
-func (o *diffOptions) Validate(cmd *cobra.Command, args []string) error {
+func (o *diffOptions) Validate(args []string) error {
 	if len(args) > 1 {
 		return errors.New("specify one path to " + constants.KustomizationFileName)
 	}
@@ -66,14 +65,8 @@ func (o *diffOptions) Validate(cmd *cobra.Command, args []string) error {
 	return nil
 }
 
-// RunDiff gets the differences between Application.Resources() and Application.RawResources().
+// RunDiff gets the differences between Application.MakeCustomizedResMap() and Application.MakeUncustomizedResMap().
 func (o *diffOptions) RunDiff(out, errOut io.Writer, fs fs.FileSystem) error {
-	printer := util.Printer{}
-	diff := util.DiffProgram{
-		Exec:   exec.New(),
-		Stdout: out,
-		Stderr: errOut,
-	}
 
 	l := loader.Init([]loader.SchemeLoader{loader.NewFileLoader(fs)})
 
@@ -87,30 +80,18 @@ func (o *diffOptions) RunDiff(out, errOut io.Writer, fs fs.FileSystem) error {
 		return err
 	}
 
-	application, err := app.New(rootLoader)
+	application, err := app.NewApplication(rootLoader)
 	if err != nil {
 		return err
 	}
-	resources, err := application.Resources()
+	transformedResources, err := application.MakeCustomizedResMap()
 	if err != nil {
 		return err
 	}
-	rawResources, err := application.RawResources()
+	rawResources, err := application.MakeUncustomizedResMap()
 	if err != nil {
 		return err
 	}
 
-	transformedDir, err := util.WriteToDir(resources, "transformed", printer)
-	if err != nil {
-		return err
-	}
-	defer transformedDir.Delete()
-
-	noopDir, err := util.WriteToDir(rawResources, "noop", printer)
-	if err != nil {
-		return err
-	}
-	defer noopDir.Delete()
-
-	return diff.Run(noopDir.Name, transformedDir.Name)
+	return diff.RunDiff(rawResources, transformedResources, out, errOut)
 }

pkg/commands/diff_test.go

@@ -27,7 +27,7 @@ import (
 
 	"github.com/ghodss/yaml"
 
-	"github.com/kubernetes-sigs/kustomize/pkg/util/fs"
+	"github.com/kubernetes-sigs/kustomize/pkg/fs"
 	"k8s.io/apimachinery/pkg/util/sets"
 )
 
@@ -74,51 +74,57 @@ func TestDiff(t *testing.T) {
 
 	for _, testcaseName := range testcases.List() {
 		t.Run(testcaseName, func(t *testing.T) {
-			name := testcaseName
-			testcase := DiffTestCase{}
-			testcaseDir := filepath.Join("testdata", "testcase-"+name)
-			testcaseData, err := ioutil.ReadFile(filepath.Join(testcaseDir, "test.yaml"))
-			if err != nil {
-				t.Fatalf("%s: %v", name, err)
-			}
-			if err := yaml.Unmarshal(testcaseData, &testcase); err != nil {
-				t.Fatalf("%s: %v", name, err)
-			}
-
-			diffOps := &diffOptions{
-				kustomizationPath: testcase.Filename,
-			}
-			buf := bytes.NewBuffer([]byte{})
-			err = diffOps.RunDiff(buf, os.Stderr, fs)
-			switch {
-			case err != nil && len(testcase.ExpectedError) == 0:
-				t.Errorf("unexpected error: %v", err)
-			case err != nil && len(testcase.ExpectedError) != 0:
-				if !strings.Contains(err.Error(), testcase.ExpectedError) {
-					t.Errorf("expected error to contain %q but got: %v", testcase.ExpectedError, err)
-				}
-				return
-			case err == nil && len(testcase.ExpectedError) != 0:
-				t.Errorf("unexpected no error")
-			}
-
-			actualString := string(buf.Bytes())
-			actualString = noopDir.ReplaceAllString(actualString, "/tmp/noop/")
-			actualString = transformedDir.ReplaceAllString(actualString, "/tmp/transformed/")
-			actualString = timestamp.ReplaceAllString(actualString, "YYYY-MM-DD HH:MM:SS")
-			actualBytes := []byte(actualString)
-			if !updateKustomizeExpected {
-				expectedBytes, err := ioutil.ReadFile(testcase.ExpectedDiff)
-				if err != nil {
-					t.Errorf("unexpected error: %v", err)
-				}
-				if !reflect.DeepEqual(actualBytes, expectedBytes) {
-					t.Errorf("%s\ndoesn't equal expected:\n%s\n", actualBytes, expectedBytes)
-				}
-			} else {
-				ioutil.WriteFile(testcase.ExpectedDiff, actualBytes, 0644)
-			}
-
+			runDiffTestCase(t, testcaseName, updateKustomizeExpected, fs,
+				noopDir, transformedDir, timestamp)
 		})
 	}
 }
+
+func runDiffTestCase(t *testing.T, testcaseName string, updateKustomizeExpected bool, fs fs.FileSystem,
+	noopDir, transformedDir, timestamp *regexp.Regexp) {
+	name := testcaseName
+	testcase := DiffTestCase{}
+	testcaseDir := filepath.Join("testdata", "testcase-"+name)
+	testcaseData, err := ioutil.ReadFile(filepath.Join(testcaseDir, "test.yaml"))
+	if err != nil {
+		t.Fatalf("%s: %v", name, err)
+	}
+	if err := yaml.Unmarshal(testcaseData, &testcase); err != nil {
+		t.Fatalf("%s: %v", name, err)
+	}
+
+	diffOps := &diffOptions{
+		kustomizationPath: testcase.Filename,
+	}
+	buf := bytes.NewBuffer([]byte{})
+	err = diffOps.RunDiff(buf, os.Stderr, fs)
+	switch {
+	case err != nil && len(testcase.ExpectedError) == 0:
+		t.Errorf("unexpected error: %v", err)
+	case err != nil && len(testcase.ExpectedError) != 0:
+		if !strings.Contains(err.Error(), testcase.ExpectedError) {
+			t.Errorf("expected error to contain %q but got: %v", testcase.ExpectedError, err)
+		}
+		return
+	case err == nil && len(testcase.ExpectedError) != 0:
+		t.Errorf("unexpected no error")
+	}
+
+	actualString := string(buf.Bytes())
+	actualString = noopDir.ReplaceAllString(actualString, "/tmp/noop/")
+	actualString = transformedDir.ReplaceAllString(actualString, "/tmp/transformed/")
+	actualString = timestamp.ReplaceAllString(actualString, "YYYY-MM-DD HH:MM:SS")
+	actualBytes := []byte(actualString)
+	if !updateKustomizeExpected {
+		expectedBytes, err := ioutil.ReadFile(testcase.ExpectedDiff)
+		if err != nil {
+			t.Errorf("unexpected error: %v", err)
+		}
+		if !reflect.DeepEqual(actualBytes, expectedBytes) {
+			t.Errorf("%s\ndoesn't equal expected:\n%s\n", actualBytes, expectedBytes)
+		}
+	} else {
+		ioutil.WriteFile(testcase.ExpectedDiff, actualBytes, 0644)
+	}
+
+}

pkg/commands/init.go

@@ -1,96 +0,0 @@
-/*
-Copyright 2017 The Kubernetes Authors.
-
-Licensed under the Apache License, Version 2.0 (the "License");
-you may not use this file except in compliance with the License.
-You may obtain a copy of the License at
-
-    http://www.apache.org/licenses/LICENSE-2.0
-
-Unless required by applicable law or agreed to in writing, software
-distributed under the License is distributed on an "AS IS" BASIS,
-WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-See the License for the specific language governing permissions and
-limitations under the License.
-*/
-
-package commands
-
-import (
-	"fmt"
-	"io"
-
-	"errors"
-
-	"github.com/kubernetes-sigs/kustomize/pkg/constants"
-	"github.com/kubernetes-sigs/kustomize/pkg/util/fs"
-	"github.com/spf13/cobra"
-)
-
-const kustomizationTemplate = `
-namePrefix: some-prefix
-# Labels to add to all objects and selectors.
-# These labels would also be used to form the selector for apply --prune
-# Named differently than “labels” to avoid confusion with metadata for this object
-commonLabels:
-  app: helloworld
-commonAnnotations:
-  note: This is an example annotation
-resources: []
-#- service.yaml
-#- ../some-dir/
-# There could also be configmaps in Base, which would make these overlays
-configMapGenerator: []
-# There could be secrets in Base, if just using a fork/rebase workflow
-secretGenerator: []
-`
-
-type initOptions struct {
-}
-
-// NewCmdInit makes the init command.
-func newCmdInit(out, errOut io.Writer, fs fs.FileSystem) *cobra.Command {
-	var o initOptions
-
-	cmd := &cobra.Command{
-		Use:   "init",
-		Short: "Creates a file called \"" + constants.KustomizationFileName + "\" in the current directory",
-		Long: "Creates a file called \"" +
-			constants.KustomizationFileName + "\" in the current directory with example values.",
-		Example:      `init`,
-		SilenceUsage: true,
-		RunE: func(cmd *cobra.Command, args []string) error {
-			err := o.Validate(cmd, args)
-			if err != nil {
-				return err
-			}
-			err = o.Complete(cmd, args)
-			if err != nil {
-				return err
-			}
-			return o.RunInit(out, errOut, fs)
-		},
-	}
-	return cmd
-}
-
-// Validate validates init command.
-func (o *initOptions) Validate(cmd *cobra.Command, args []string) error {
-	if len(args) > 0 {
-		return errors.New("The init command takes no arguments.")
-	}
-	return nil
-}
-
-// Complete completes init command.
-func (o *initOptions) Complete(cmd *cobra.Command, args []string) error {
-	return nil
-}
-
-// RunInit writes a kustomization file.
-func (o *initOptions) RunInit(out, errOut io.Writer, fs fs.FileSystem) error {
-	if _, err := fs.Stat(constants.KustomizationFileName); err == nil {
-		return fmt.Errorf("%q already exists", constants.KustomizationFileName)
-	}
-	return fs.WriteFile(constants.KustomizationFileName, []byte(kustomizationTemplate))
-}

pkg/commands/kustomizationfile.go

@@ -25,9 +25,9 @@ import (
 	"github.com/ghodss/yaml"
 
 	"github.com/kubernetes-sigs/kustomize/pkg/constants"
+	"github.com/kubernetes-sigs/kustomize/pkg/fs"
 	interror "github.com/kubernetes-sigs/kustomize/pkg/internal/error"
 	"github.com/kubernetes-sigs/kustomize/pkg/types"
-	"github.com/kubernetes-sigs/kustomize/pkg/util/fs"
 )
 
 type kustomizationFile struct {
@@ -35,7 +35,7 @@ type kustomizationFile struct {
 	fsys fs.FileSystem
 }
 
-func newKustomizationFile(mPath string, fsys fs.FileSystem) (*kustomizationFile, error) {
+func newKustomizationFile(mPath string, fsys fs.FileSystem) (*kustomizationFile, error) { // nolint
 	mf := &kustomizationFile{path: mPath, fsys: fsys}
 	err := mf.validate()
 	if err != nil {
@@ -61,7 +61,7 @@ func (mf *kustomizationFile) validate() error {
 		}
 	} else {
 		if !strings.HasSuffix(mf.path, constants.KustomizationFileName) {
-			errorMsg := fmt.Sprintf("Kustomization file path (%s) should have %s suffix\n", mf.path, constants.KustomizationSuffix)
+			errorMsg := fmt.Sprintf("Kustomization file path (%s) should have %s suffix\n", mf.path, constants.KustomizationFileSuffix)
 			merr := interror.KustomizationError{KustomizationPath: mf.path, ErrorMsg: errorMsg}
 			return merr
 		}

pkg/commands/kustomizationfile_test.go

@@ -22,8 +22,8 @@ import (
 	"testing"
 
 	"github.com/kubernetes-sigs/kustomize/pkg/constants"
+	"github.com/kubernetes-sigs/kustomize/pkg/fs"
 	"github.com/kubernetes-sigs/kustomize/pkg/types"
-	"github.com/kubernetes-sigs/kustomize/pkg/util/fs"
 )
 
 func TestWriteAndRead(t *testing.T) {

pkg/commands/set_name_prefix.go

@@ -18,12 +18,11 @@ package commands
 
 import (
 	"errors"
-	"io"
 
 	"github.com/spf13/cobra"
 
 	"github.com/kubernetes-sigs/kustomize/pkg/constants"
-	"github.com/kubernetes-sigs/kustomize/pkg/util/fs"
+	"github.com/kubernetes-sigs/kustomize/pkg/fs"
 )
 
 type setNamePrefixOptions struct {
@@ -31,7 +30,7 @@ type setNamePrefixOptions struct {
 }
 
 // newCmdSetNamePrefix sets the value of the namePrefix field in the kustomization.
-func newCmdSetNamePrefix(out, errOut io.Writer, fsys fs.FileSystem) *cobra.Command {
+func newCmdSetNamePrefix(fsys fs.FileSystem) *cobra.Command {
 	var o setNamePrefixOptions
 
 	cmd := &cobra.Command{
@@ -52,7 +51,7 @@ and overwrite the value with "acme-" if the field does exist.
 			if err != nil {
 				return err
 			}
-			return o.RunSetNamePrefix(out, errOut, fsys)
+			return o.RunSetNamePrefix(fsys)
 		},
 	}
 	return cmd
@@ -74,7 +73,7 @@ func (o *setNamePrefixOptions) Complete(cmd *cobra.Command, args []string) error
 }
 
 // RunSetNamePrefix runs setNamePrefix command (does real work).
-func (o *setNamePrefixOptions) RunSetNamePrefix(out, errOut io.Writer, fsys fs.FileSystem) error {
+func (o *setNamePrefixOptions) RunSetNamePrefix(fsys fs.FileSystem) error {
 	mf, err := newKustomizationFile(constants.KustomizationFileName, fsys)
 	if err != nil {
 		return err

pkg/commands/set_name_prefix_test.go

@@ -17,14 +17,12 @@ limitations under the License.
 package commands
 
 import (
-	"bytes"
-	"os"
 	"testing"
 
 	"strings"
 
 	"github.com/kubernetes-sigs/kustomize/pkg/constants"
-	"github.com/kubernetes-sigs/kustomize/pkg/util/fs"
+	"github.com/kubernetes-sigs/kustomize/pkg/fs"
 )
 
 const (
@@ -32,11 +30,10 @@ const (
 )
 
 func TestSetNamePrefixHappyPath(t *testing.T) {
-	buf := bytes.NewBuffer([]byte{})
 	fakeFS := fs.MakeFakeFS()
 	fakeFS.WriteFile(constants.KustomizationFileName, []byte(kustomizationContent))
 
-	cmd := newCmdSetNamePrefix(buf, os.Stderr, fakeFS)
+	cmd := newCmdSetNamePrefix(fakeFS)
 	args := []string{goodPrefixValue}
 	err := cmd.RunE(cmd, args)
 	if err != nil {
@@ -52,10 +49,9 @@ func TestSetNamePrefixHappyPath(t *testing.T) {
 }
 
 func TestSetNamePrefixNoArgs(t *testing.T) {
-	buf := bytes.NewBuffer([]byte{})
 	fakeFS := fs.MakeFakeFS()
 
-	cmd := newCmdSetNamePrefix(buf, os.Stderr, fakeFS)
+	cmd := newCmdSetNamePrefix(fakeFS)
 	err := cmd.Execute()
 	if err == nil {
 		t.Errorf("expected error: %v", err)

pkg/commands/testdata/testcase-base-only/in/kustomization.yaml

@@ -6,5 +6,4 @@ commonLabels:
 commonAnnotations:
   note: This is a test annotation
 resources:
-  - deployment.yaml
-  - service.yaml
+  - resources/*.yaml

pkg/commands/testdata/testcase-configmaps/base/myapp/mycomponent/kustomization.yaml

@@ -0,0 +1,6 @@
+namePrefix: p1-
+configMapGenerator:
+- name: com1
+  behavior: create
+  literals:
+    - from=base

pkg/commands/testdata/testcase-configmaps/base/myapp/mycomponent2/kustomization.yaml

@@ -0,0 +1,6 @@
+namePrefix: p2-
+configMapGenerator:
+- name: com2
+  behavior: create
+  literals:
+    - from=base

pkg/commands/testdata/testcase-configmaps/expected.diff

@@ -0,0 +1,16 @@
+diff -u -N /tmp/noop/v1_ConfigMap_com1.yaml /tmp/transformed/v1_ConfigMap_com1.yaml
+--- /tmp/noop/v1_ConfigMap_com1.yaml	YYYY-MM-DD HH:MM:SS
++++ /tmp/transformed/v1_ConfigMap_com1.yaml	YYYY-MM-DD HH:MM:SS
+@@ -1,9 +1,11 @@
+ apiVersion: v1
+ data:
++  baz: qux
++  foo: bar
+   from: overlay
+ kind: ConfigMap
+ metadata:
+   annotations: {}
+   creationTimestamp: null
+   labels: {}
+-  name: p1-com1-cmdb776d5b
++  name: p1-com1-dhbbm922gd

pkg/commands/testdata/testcase-configmaps/expected.yaml

@@ -0,0 +1,21 @@
+apiVersion: v1
+data:
+  baz: qux
+  foo: bar
+  from: overlay
+kind: ConfigMap
+metadata:
+  annotations: {}
+  creationTimestamp: null
+  labels: {}
+  name: p1-com1-dhbbm922gd
+---
+apiVersion: v1
+data:
+  from: overlay
+kind: ConfigMap
+metadata:
+  annotations: {}
+  creationTimestamp: null
+  labels: {}
+  name: p2-com2-c4b8md75k9

pkg/commands/testdata/testcase-configmaps/overlay/dev/kustomization.yaml

@@ -0,0 +1,9 @@
+bases:
+- myapp/mycomponent
+- myapp/mycomponent2
+configMapGenerator:
+- name: com1
+  behavior: merge
+  literals:
+    - foo=bar
+    - baz=qux

pkg/commands/testdata/testcase-configmaps/overlay/dev/myapp/mycomponent/kustomization.yaml

@@ -0,0 +1,7 @@
+bases:
+- ../../../../base/myapp/mycomponent
+configMapGenerator:
+- name: com1
+  behavior: merge
+  literals:
+    - from=overlay

pkg/commands/testdata/testcase-configmaps/overlay/dev/myapp/mycomponent2/kustomization.yaml

@@ -0,0 +1,7 @@
+bases:
+- ../../../../base/myapp/mycomponent2
+configMapGenerator:
+- name: com2
+  behavior: merge
+  literals:
+    - from=overlay

pkg/commands/testdata/testcase-configmaps/test.yaml

@@ -0,0 +1,5 @@
+description: configmap generator overlay
+args: []
+filename: testdata/testcase-configmaps/overlay/dev
+expectedStdout: testdata/testcase-configmaps/expected.yaml
+expectedDiff: testdata/testcase-configmaps/expected.diff

pkg/commands/testdata/testcase-crds/crd/bee.yaml

@@ -0,0 +1,6 @@
+apiVersion: v1beta1
+kind: Bee
+metadata:
+  name: bee
+spec:
+  action: fly

pkg/commands/testdata/testcase-crds/crd/kustomization.yaml

@@ -0,0 +1,9 @@
+crds:
+- mycrd.json
+
+resources:
+- secret.yaml
+- mykind.yaml
+- bee.yaml
+
+namePrefix: test-

pkg/commands/testdata/testcase-crds/crd/mycrd.json

@@ -0,0 +1,170 @@
+{
+  "github.com/example/pkg/apis/jingfang/v1beta1.Bee": {
+    "Schema": {
+      "description": "Bee",
+      "properties": {
+        "apiVersion": {
+          "description": "APIVersion defines the versioned schema of this representation of an object. Servers should convert recognized schemas to the latest internal value, and may reject unrecognized values. More info: https://git.k8s.io/community/contributors/devel/api-conventions.md#resources",
+          "type": "string"
+        },
+        "kind": {
+          "description": "Kind is a string value representing the REST resource this object represents. Servers may infer this from the endpoint the client submits requests to. Cannot be updated. In CamelCase. More info: https://git.k8s.io/community/contributors/devel/api-conventions.md#types-kinds",
+          "type": "string"
+        },
+        "metadata": {
+          "$ref": "k8s.io/apimachinery/pkg/apis/meta/v1.ObjectMeta"
+        },
+        "spec": {
+          "$ref": "github.com/example/pkg/apis/jingfang/v1beta1.BeeSpec"
+        },
+        "status": {
+          "$ref": "github.com/example/pkg/apis/jingfang/v1beta1.BeeStatus"
+        }
+      }
+    },
+    "Dependencies": [
+      "github.com/example/pkg/apis/jingfang/v1beta1.BeeSpec",
+      "github.com/example/pkg/apis/jingfang/v1beta1.BeeStatus",
+      "k8s.io/apimachinery/pkg/apis/meta/v1.ObjectMeta"
+    ]
+  },
+  "github.com/example/pkg/apis/jingfang/v1beta1.BeeList": {
+    "Schema": {
+      "required": [
+        "items"
+      ],
+      "properties": {
+        "apiVersion": {
+          "description": "APIVersion defines the versioned schema of this representation of an object. Servers should convert recognized schemas to the latest internal value, and may reject unrecognized values. More info: https://git.k8s.io/community/contributors/devel/api-conventions.md#resources",
+          "type": "string"
+        },
+        "items": {
+          "type": "array",
+          "items": {
+            "$ref": "github.com/example/pkg/apis/jingfang/v1beta1.Bee"
+          }
+        },
+        "kind": {
+          "description": "Kind is a string value representing the REST resource this object represents. Servers may infer this from the endpoint the client submits requests to. Cannot be updated. In CamelCase. More info: https://git.k8s.io/community/contributors/devel/api-conventions.md#types-kinds",
+          "type": "string"
+        },
+        "metadata": {
+          "$ref": "k8s.io/apimachinery/pkg/apis/meta/v1.ListMeta"
+        }
+      }
+    },
+    "Dependencies": [
+      "github.com/example/pkg/apis/jingfang/v1beta1.Bee",
+      "k8s.io/apimachinery/pkg/apis/meta/v1.ListMeta"
+    ]
+  },
+  "github.com/example/pkg/apis/jingfang/v1beta1.BeeObjectReference": {
+    "Schema": {
+      "properties": {
+        "name": {
+          "type": "string"
+        }
+      }
+    },
+    "Dependencies": []
+  },
+  "github.com/example/pkg/apis/jingfang/v1beta1.BeeSpec": {
+    "Schema": {
+      "description": "BeeSpec defines the desired state of Bee"
+    },
+    "Dependencies": []
+  },
+  "github.com/example/pkg/apis/jingfang/v1beta1.BeeStatus": {
+    "Schema": {
+      "description": "BeeStatus defines the observed state of Bee"
+    },
+    "Dependencies": []
+  },
+  "github.com/example/pkg/apis/jingfang/v1beta1.MyKind": {
+    "Schema": {
+      "description": "MyKind",
+      "properties": {
+        "apiVersion": {
+          "description": "APIVersion defines the versioned schema of this representation of an object. Servers should convert recognized schemas to the latest internal value, and may reject unrecognized values. More info: https://git.k8s.io/community/contributors/devel/api-conventions.md#resources",
+          "type": "string"
+        },
+        "kind": {
+          "description": "Kind is a string value representing the REST resource this object represents. Servers may infer this from the endpoint the client submits requests to. Cannot be updated. In CamelCase. More info: https://git.k8s.io/community/contributors/devel/api-conventions.md#types-kinds",
+          "type": "string"
+        },
+        "metadata": {
+          "$ref": "k8s.io/apimachinery/pkg/apis/meta/v1.ObjectMeta"
+        },
+        "spec": {
+          "$ref": "github.com/example/pkg/apis/jingfang/v1beta1.MyKindSpec"
+        },
+        "status": {
+          "$ref": "github.com/example/pkg/apis/jingfang/v1beta1.MyKindStatus"
+        }
+      }
+    },
+    "Dependencies": [
+      "github.com/example/pkg/apis/jingfang/v1beta1.MyKindSpec",
+      "github.com/example/pkg/apis/jingfang/v1beta1.MyKindStatus",
+      "k8s.io/apimachinery/pkg/apis/meta/v1.ObjectMeta"
+    ]
+  },
+  "github.com/example/pkg/apis/jingfang/v1beta1.MyKindList": {
+    "Schema": {
+      "required": [
+        "items"
+      ],
+      "properties": {
+        "apiVersion": {
+          "description": "APIVersion defines the versioned schema of this representation of an object. Servers should convert recognized schemas to the latest internal value, and may reject unrecognized values. More info: https://git.k8s.io/community/contributors/devel/api-conventions.md#resources",
+          "type": "string"
+        },
+        "items": {
+          "type": "array",
+          "items": {
+            "$ref": "github.com/example/pkg/apis/jingfang/v1beta1.MyKind"
+          }
+        },
+        "kind": {
+          "description": "Kind is a string value representing the REST resource this object represents. Servers may infer this from the endpoint the client submits requests to. Cannot be updated. In CamelCase. More info: https://git.k8s.io/community/contributors/devel/api-conventions.md#types-kinds",
+          "type": "string"
+        },
+        "metadata": {
+          "$ref": "k8s.io/apimachinery/pkg/apis/meta/v1.ListMeta"
+        }
+      }
+    },
+    "Dependencies": [
+      "github.com/example/pkg/apis/jingfang/v1beta1.MyKind",
+      "k8s.io/apimachinery/pkg/apis/meta/v1.ListMeta"
+    ]
+  },
+  "github.com/example/pkg/apis/jingfang/v1beta1.MyKindSpec": {
+    "Schema": {
+      "description": "MyKindSpec defines the desired state of MyKind",
+      "properties": {
+        "beeRef": {
+          "x-kubernetes-object-ref-api-version": "v1beta1",
+          "x-kubernetes-object-ref-kind": "Bee",
+          "$ref": "github.com/example/pkg/apis/jingfang/v1beta1.BeeObjectReference"
+        },
+        "secretRef": {
+          "description": "If defined, we use this secret for configuring the MYSQL_ROOT_PASSWORD If it is not set we generate a secret dynamically",
+          "x-kubernetes-object-ref-api-version": "v1",
+          "x-kubernetes-object-ref-kind": "Secret",
+          "$ref": "k8s.io/api/core/v1.LocalObjectReference"
+        }
+      }
+    },
+    "Dependencies": [
+      "github.com/example/pkg/apis/jingfang/v1beta1.BeeObjectReference",
+      "k8s.io/api/core/v1.LocalObjectReference"
+    ]
+  },
+  "github.com/example/pkg/apis/jingfang/v1beta1.MyKindStatus": {
+    "Schema": {
+      "description": "MyKindStatus defines the observed state of MyKind"
+    },
+    "Dependencies": []
+  }
+}

pkg/commands/testdata/testcase-crds/crd/mykind.yaml

@@ -0,0 +1,9 @@
+apiVersion: jingfang.example.com/v1beta1
+kind: MyKind
+metadata:
+  name: mykind
+spec:
+  secretRef:
+    name: crdsecret
+  beeRef:
+    name: bee

pkg/commands/testdata/testcase-crds/crd/secret.yaml

@@ -0,0 +1,6 @@
+apiVersion: v1
+kind: Secret
+metadata:
+  name: crdsecret
+data:
+  PATH: YmJiYmJiYmIK

pkg/commands/testdata/testcase-crds/expected.diff

@@ -0,0 +1,36 @@
+diff -u -N /tmp/noop/jingfang.example.com_v1beta1_MyKind_mykind.yaml /tmp/transformed/jingfang.example.com_v1beta1_MyKind_mykind.yaml
+--- /tmp/noop/jingfang.example.com_v1beta1_MyKind_mykind.yaml	YYYY-MM-DD HH:MM:SS
++++ /tmp/transformed/jingfang.example.com_v1beta1_MyKind_mykind.yaml	YYYY-MM-DD HH:MM:SS
+@@ -1,9 +1,9 @@
+ apiVersion: jingfang.example.com/v1beta1
+ kind: MyKind
+ metadata:
+-  name: mykind
++  name: test-mykind
+ spec:
+   beeRef:
+-    name: bee
++    name: test-bee
+   secretRef:
+-    name: crdsecret-m5ht5thcb4
++    name: test-crdsecret-m48btmkck5
+diff -u -N /tmp/noop/v1beta1_Bee_bee.yaml /tmp/transformed/v1beta1_Bee_bee.yaml
+--- /tmp/noop/v1beta1_Bee_bee.yaml	YYYY-MM-DD HH:MM:SS
++++ /tmp/transformed/v1beta1_Bee_bee.yaml	YYYY-MM-DD HH:MM:SS
+@@ -1,6 +1,6 @@
+ apiVersion: v1beta1
+ kind: Bee
+ metadata:
+-  name: bee
++  name: test-bee
+ spec:
+   action: fly
+diff -u -N /tmp/noop/v1_Secret_crdsecret.yaml /tmp/transformed/v1_Secret_crdsecret.yaml
+--- /tmp/noop/v1_Secret_crdsecret.yaml	YYYY-MM-DD HH:MM:SS
++++ /tmp/transformed/v1_Secret_crdsecret.yaml	YYYY-MM-DD HH:MM:SS
+@@ -3,4 +3,4 @@
+   PATH: YmJiYmJiYmIK
+ kind: Secret
+ metadata:
+-  name: crdsecret-m5ht5thcb4
++  name: test-crdsecret-m48btmkck5

pkg/commands/testdata/testcase-crds/expected.yaml

@@ -0,0 +1,23 @@
+apiVersion: v1
+data:
+  PATH: YmJiYmJiYmIK
+kind: Secret
+metadata:
+  name: test-crdsecret-m48btmkck5
+---
+apiVersion: v1beta1
+kind: Bee
+metadata:
+  name: test-bee
+spec:
+  action: fly
+---
+apiVersion: jingfang.example.com/v1beta1
+kind: MyKind
+metadata:
+  name: test-mykind
+spec:
+  beeRef:
+    name: test-bee
+  secretRef:
+    name: test-crdsecret-m48btmkck5