fix(shared): stop ancestor discovery at worktree root

Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-openagent)

Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>

src/shared/project-discovery-dirs.ts

@@ -1,13 +1,29 @@
-import { existsSync } from "node:fs"
+import { execFileSync } from "node:child_process"
+import { existsSync, realpathSync } from "node:fs"
 import { dirname, join, resolve } from "node:path"
 
+function normalizePath(path: string): string {
+  const resolvedPath = resolve(path)
+  if (!existsSync(resolvedPath)) {
+    return resolvedPath
+  }
+
+  try {
+    return realpathSync(resolvedPath)
+  } catch {
+    return resolvedPath
+  }
+}
+
 function findAncestorDirectories(
   startDirectory: string,
   targetPaths: ReadonlyArray<ReadonlyArray<string>>,
+  stopDirectory?: string,
 ): string[] {
   const directories: string[] = []
   const seen = new Set<string>()
-  let currentDirectory = resolve(startDirectory)
+  let currentDirectory = normalizePath(startDirectory)
+  const resolvedStopDirectory = stopDirectory ? normalizePath(stopDirectory) : undefined
 
   while (true) {
     for (const targetPath of targetPaths) {
@@ -20,33 +36,66 @@ function findAncestorDirectories(
       directories.push(candidateDirectory)
     }
 
+    if (resolvedStopDirectory === currentDirectory) {
+      return directories
+    }
+
     const parentDirectory = dirname(currentDirectory)
     if (parentDirectory === currentDirectory) {
       return directories
     }
 
-    currentDirectory = parentDirectory
+    currentDirectory = normalizePath(parentDirectory)
   }
 }
 
-export function findProjectClaudeSkillDirs(startDirectory: string): string[] {
-  return findAncestorDirectories(startDirectory, [[".claude", "skills"]])
+function detectWorktreePath(directory: string): string | undefined {
+  try {
+    return execFileSync("git", ["rev-parse", "--show-toplevel"], {
+      cwd: directory,
+      encoding: "utf-8",
+      timeout: 5000,
+      stdio: ["pipe", "pipe", "pipe"],
+    }).trim()
+  } catch {
+    return undefined
+  }
 }
 
-export function findProjectAgentsSkillDirs(startDirectory: string): string[] {
-  return findAncestorDirectories(startDirectory, [[".agents", "skills"]])
+export function findProjectClaudeSkillDirs(startDirectory: string, stopDirectory?: string): string[] {
+  return findAncestorDirectories(
+    startDirectory,
+    [[".claude", "skills"]],
+    stopDirectory ?? detectWorktreePath(startDirectory),
+  )
 }
 
-export function findProjectOpencodeSkillDirs(startDirectory: string): string[] {
-  return findAncestorDirectories(startDirectory, [
-    [".opencode", "skills"],
-    [".opencode", "skill"],
-  ])
+export function findProjectAgentsSkillDirs(startDirectory: string, stopDirectory?: string): string[] {
+  return findAncestorDirectories(
+    startDirectory,
+    [[".agents", "skills"]],
+    stopDirectory ?? detectWorktreePath(startDirectory),
+  )
 }
 
-export function findProjectOpencodeCommandDirs(startDirectory: string): string[] {
-  return findAncestorDirectories(startDirectory, [
-    [".opencode", "commands"],
-    [".opencode", "command"],
-  ])
+export function findProjectOpencodeSkillDirs(startDirectory: string, stopDirectory?: string): string[] {
+  return findAncestorDirectories(
+    startDirectory,
+    [
+      [".opencode", "skills"],
+      [".opencode", "skill"],
+    ],
+    stopDirectory ?? detectWorktreePath(startDirectory),
+  )
+}
+
+export function findProjectOpencodeCommandDirs(startDirectory: string, stopDirectory?: string): string[] {
+  return findAncestorDirectories(
+    startDirectory,
+    [
+      [".opencode", "commands"],
+      [".opencode", "command"],
+    ],
+    stopDirectory ?? detectWorktreePath(startDirectory),
+  )
 }