fix(installing.commands): key selectProjectByDir graph by project.rootDir (#12380)

* fix(installing.commands): key selectProjectByDir graph by project.rootDir

`selectProjectByDir` constructs a single-entry `ProjectsGraph` for the
non-workspace install path. It was using `searchedDir` (`opts.dir`) as
the key, but downstream `recursive()` builds `manifestsByPath` from the
projects array (keyed by `project.rootDir`) and then looks up entries
via `manifestsByPath[rootDir]` where `rootDir` is drawn from
`Object.keys(selectedProjectsGraph)`. When `opts.dir` and
`project.rootDir` differ in platform-normalized form (most often on
Windows due to drive-letter casing), the lookup falls through as
`undefined` and `pnpm add <pkg>` crashes with:

  Cannot destructure property 'manifest' of 'manifestsByPath[rootDir]' as it is undefined

Pin the graph key to `project.rootDir` in both `installing/commands/src/installDeps.ts`
and `installing/commands/src/import/index.ts`, so the keys stay in sync
with `manifestsByPath`. Closes https://github.com/pnpm/pnpm/issues/12379

Written by an agent (Claude Code, claude-opus-4-7).

* docs: remove redundant comments

* test(installing.commands): cover project graph keying

* Revert "test(installing.commands): cover project graph keying"

This reverts commit 426fae9434.

* test(installing.commands): cover add with mismatched project dir

---------

Co-authored-by: Zoltan Kochan <z@kochan.io>

.changeset/fix-windows-recursive-undefined-manifest.md

@@ -0,0 +1,6 @@
+---
+"@pnpm/installing.commands": patch
+"pnpm": patch
+---
+
+Fixed `Cannot destructure property 'manifest' of 'manifestsByPath[rootDir]' as it is undefined` regression introduced in 11.6.0 when running `pnpm add <pkg>` outside a workspace on Windows. `selectProjectByDir` was keying the resulting `ProjectsGraph` by `opts.dir` instead of `project.rootDir`, so downstream `manifestsByPath` lookups missed when the two paths normalized differently (typically drive-letter casing). [pnpm/pnpm#12379](https://github.com/pnpm/pnpm/issues/12379)

installing/commands/src/import/index.ts

@@ -337,7 +337,7 @@ function getAllVersionsFromYarnLockFile (
 function selectProjectByDir (projects: Project[], searchedDir: string): ProjectsGraph | undefined {
   const project = projects.find(({ rootDir }) => path.relative(rootDir, searchedDir) === '')
   if (project == null) return undefined
-  return { [searchedDir]: { dependencies: [], package: project } }
+  return { [project.rootDir]: { dependencies: [], package: project } }
 }
 
 function getYarnLockfileType (

installing/commands/src/installDeps.ts

@@ -519,7 +519,7 @@ export async function installDeps (
 function selectProjectByDir (projects: Project[], searchedDir: string): ProjectsGraph | undefined {
   const project = projects.find(({ rootDir }) => path.relative(rootDir, searchedDir) === '')
   if (project == null) return undefined
-  return { [searchedDir]: { dependencies: [], package: project } }
+  return { [project.rootDir]: { dependencies: [], package: project } }
 }
 
 async function recursiveInstallThenUpdateWorkspaceState (

installing/commands/test/add.ts

@@ -6,7 +6,7 @@ import type { PnpmError } from '@pnpm/error'
 import { add, remove } from '@pnpm/installing.commands'
 import { prepare, prepareEmpty, preparePackages } from '@pnpm/prepare'
 import { REGISTRY_MOCK_PORT } from '@pnpm/testing.registry-mock'
-import type { ProjectManifest } from '@pnpm/types'
+import type { Project, ProjectManifest, ProjectRootDir, ProjectRootDirRealPath } from '@pnpm/types'
 import { loadJsonFile } from 'load-json-file'
 import { temporaryDirectory } from 'tempy'
 
@@ -308,6 +308,41 @@ test('pnpm add automatically installs missing peer dependencies', async () => {
   expect(Object.keys(lockfile.packages)).toHaveLength(5)
 })
 
+test('pnpm add handles matching workspace project when dir differs from project.rootDir', async () => {
+  const rootProjectManifest: ProjectManifest = {
+    name: 'project',
+    version: '0.0.0',
+  }
+  const project = prepare(rootProjectManifest)
+  const rootDir = project.dir() as ProjectRootDir
+  const allProjects: Project[] = [
+    {
+      manifest: rootProjectManifest,
+      rootDir,
+      rootDirRealPath: fs.realpathSync(rootDir) as ProjectRootDirRealPath,
+      writeProjectManifest: async (manifest) => project.writePackageJson(manifest),
+    },
+  ]
+
+  await expect(add.handler({
+    ...DEFAULT_OPTIONS,
+    allProjects,
+    dir: `${rootDir}${path.sep}`,
+    linkWorkspacePackages: false,
+    lockfileDir: rootDir,
+    rootProjectManifest,
+    rootProjectManifestDir: rootDir,
+    sharedWorkspaceLockfile: true,
+    workspaceDir: rootDir,
+  }, ['is-positive@1.0.0'])).resolves.toBeUndefined()
+
+  const manifest = await loadJsonFile<ProjectManifest>(path.resolve('package.json'))
+  expect(manifest.dependencies).toStrictEqual({
+    'is-positive': '1.0.0',
+  })
+  project.has('is-positive')
+})
+
 test('add: fail when global bin directory is not found', async () => {
   prepareEmpty()