[plugins] Fix rm for packages with __remove_trigger_package (#1940)

## Summary

Fixes issue where user could not remove package that is replaced by a
flake in plugin (uses `__remove_trigger_package`)

Fixes #1936

We need two different functions for packages:

* `AllPackages` which is used for instalation and lock file. Includes
packages added/removed by plugins.
* `TopLevelPackages` is only what is in root devbox.json

## How was it tested?

* Tested manually
* Added php to rm unit test

Author: mikeland73

internal/devbox/devbox.go

@@ -176,7 +176,7 @@ func (d *Devbox) ConfigHash() (string, error) {
 
 	buf := bytes.Buffer{}
 	buf.WriteString(h)
-	for _, pkg := range d.ConfigPackages() {
+	for _, pkg := range d.AllPackages() {
 		buf.WriteString(pkg.Hash())
 	}
 	for _, pluginConfig := range d.cfg.IncludedPluginConfigs() {
@@ -1033,21 +1033,27 @@ func (d *Devbox) PackageNames() []string {
 	return d.cfg.PackagesVersionedNames()
 }
 
-// ConfigPackages returns the packages that are defined in devbox.json
-// NOTE: the return type is different from devconfig.Packages
-func (d *Devbox) ConfigPackages() []*devpkg.Package {
+// AllPackages returns the packages that are defined in devbox.json and
+// recursively added by plugins.
+// NOTE: This will not return packages removed by their plugin with the
+// __remove_trigger_package field.
+func (d *Devbox) AllPackages() []*devpkg.Package {
 	return devpkg.PackagesFromConfig(d.cfg.Packages(), d.lockfile)
 }
 
+func (d *Devbox) TopLevelPackages() []*devpkg.Package {
+	return devpkg.PackagesFromConfig(d.cfg.Root.TopLevelPackages(), d.lockfile)
+}
+
 // InstallablePackages returns the packages that are to be installed
 func (d *Devbox) InstallablePackages() []*devpkg.Package {
-	return lo.Filter(d.ConfigPackages(), func(pkg *devpkg.Package, _ int) bool {
+	return lo.Filter(d.AllPackages(), func(pkg *devpkg.Package, _ int) bool {
 		return pkg.IsInstallable()
 	})
 }
 
 func (d *Devbox) HasDeprecatedPackages() bool {
-	for _, pkg := range d.ConfigPackages() {
+	for _, pkg := range d.AllPackages() {
 		if pkg.IsLegacy() {
 			return true
 		}
@@ -1060,7 +1066,7 @@ func (d *Devbox) findPackageByName(name string) (*devpkg.Package, error) {
 		return nil, errors.New("package name cannot be empty")
 	}
 	results := map[*devpkg.Package]bool{}
-	for _, pkg := range d.ConfigPackages() {
+	for _, pkg := range d.TopLevelPackages() {
 		if pkg.Raw == name || pkg.CanonicalName() == name {
 			results[pkg] = true
 		}

internal/devbox/docgen/docgen.go

@@ -56,7 +56,8 @@ func GenerateReadme(
 		"Scripts":     devbox.Config().Scripts(),
 		"EnvVars":     devbox.Config().Env(),
 		"InitHook":    devbox.Config().InitHook(),
-		"Packages":    devbox.ConfigPackages(),
+		"Packages":    devbox.TopLevelPackages(),
+		// TODO add includes
 	})
 }
 

internal/devbox/packages.go

@@ -294,7 +294,7 @@ func (d *Devbox) updateLockfile(recomputeState bool) error {
 	d.lockfile.Tidy()
 
 	// Update lockfile with new packages that are not to be installed
-	for _, pkg := range d.ConfigPackages() {
+	for _, pkg := range d.AllPackages() {
 		if err := pkg.EnsureUninstallableIsInLockfile(); err != nil {
 			return err
 		}

internal/devbox/update.go

@@ -81,7 +81,7 @@ func (d *Devbox) inputsToUpdate(
 	opts devopt.UpdateOpts,
 ) ([]*devpkg.Package, error) {
 	if len(opts.Pkgs) == 0 {
-		return d.ConfigPackages(), nil
+		return d.AllPackages(), nil
 	}
 
 	var pkgsToUpdate []*devpkg.Package

testscripts/rm/add-rm.test.txt

@@ -1,20 +1,20 @@
 exec devbox init
 
-exec devbox add hello vim cowsay
+exec devbox add hello vim cowsay php
 json.superset devbox.json all.json
 
-exec devbox rm vim hello
+exec devbox rm vim hello php
 json.superset devbox.json cowsay.json
 
-exec devbox add vim hello vim hello vim hello vim hello cowsay
+exec devbox add vim hello vim hello vim hello vim hello cowsay php php
 json.superset devbox.json all.json
 
-exec devbox rm vim hello cowsay cowsay
+exec devbox rm vim hello cowsay cowsay php
 json.superset devbox.json empty.json
 
 -- all.json --
 {
-  "packages": ["hello@latest", "vim@latest", "cowsay@latest"]
+  "packages": ["hello@latest", "vim@latest", "cowsay@latest", "php@latest"]
 }
 
 -- cowsay.json --