fix: detect worktree paths resolved through .gsd symlinks (#1585)

When .gsd is a symlink (e.g., openclip/.gsd -> ~/.gsd/projects/<hash>),
worktrees resolve to ~/.gsd/projects/<hash>/worktrees/<name> instead of
the expected <repo>/.gsd/worktrees/<name>. All worktree detection
functions used the marker /.gsd/worktrees/ which did not match the
resolved path /.gsd/projects/<hash>/worktrees/.

This caused three cascading failures:
1. escapeStaleWorktree failed to detect stale worktree CWD
2. isUnderGsdWorktrees returned false, causing nested worktrees
3. Empty registry was conflated with "all milestones complete"

Changes:
- Add findWorktreeSegment helper matching both direct and symlink layouts
- Refactor detectWorktreeName and resolveProjectRoot to use the helper
- Fix escapeStaleWorktree in auto-worktree-sync.ts for symlink paths
- Fix isUnderGsdWorktrees in auto-start.ts for symlink paths
- Fix resolveCapturesPath in captures.ts for symlink paths
- Distinguish empty registry from all-complete in auto-loop.ts
- Add tests for symlink-resolved path detection

src/resources/extensions/gsd/auto-loop.ts

@@ -787,7 +787,7 @@ export async function autoLoop(
           (m: { status: string }) =>
             m.status !== "complete" && m.status !== "parked",
         );
-        if (incomplete.length === 0) {
+        if (incomplete.length === 0 && state.registry.length > 0) {
           // All milestones complete — merge milestone branch before stopping
           if (s.currentMilestoneId) {
             deps.resolver.mergeAndExit(s.currentMilestoneId, ctx.ui);
@@ -804,6 +804,18 @@ export async function autoLoop(
             "success",
           );
           await deps.stopAuto(ctx, pi, "All milestones complete");
+        } else if (incomplete.length === 0 && state.registry.length === 0) {
+          // Empty registry — no milestones visible, likely a path resolution bug
+          const diag = `basePath=${s.basePath}, phase=${state.phase}`;
+          ctx.ui.notify(
+            `No milestones visible in current scope. Possible path resolution issue.\n   Diagnostic: ${diag}`,
+            "error",
+          );
+          await deps.stopAuto(
+            ctx,
+            pi,
+            `No milestones found — check basePath resolution`,
+          );
         } else if (state.phase === "blocked") {
           const blockerMsg = `Blocked: ${state.blockers.join(", ")}`;
           await deps.stopAuto(ctx, pi, blockerMsg);

src/resources/extensions/gsd/auto-start.ts

@@ -429,10 +429,16 @@ export async function bootstrapAutoSession(
     s.originalBasePath = base;
 
     const isUnderGsdWorktrees = (p: string): boolean => {
+      // Direct layout: /.gsd/worktrees/
       const marker = `${pathSep}.gsd${pathSep}worktrees${pathSep}`;
       if (p.includes(marker)) return true;
       const worktreesSuffix = `${pathSep}.gsd${pathSep}worktrees`;
-      return p.endsWith(worktreesSuffix);
+      if (p.endsWith(worktreesSuffix)) return true;
+      // Symlink-resolved layout: /.gsd/projects/<hash>/worktrees/
+      const symlinkRe = new RegExp(
+        `\\${pathSep}\\.gsd\\${pathSep}projects\\${pathSep}[a-f0-9]+\\${pathSep}worktrees(?:\\${pathSep}|$)`,
+      );
+      return symlinkRe.test(p);
     };
 
     if (

src/resources/extensions/gsd/auto-worktree-sync.ts

@@ -153,9 +153,18 @@ export function checkResourcesStale(
  * Returns the corrected base path.
  */
 export function escapeStaleWorktree(base: string): string {
-  const marker = `${pathSep}.gsd${pathSep}worktrees${pathSep}`;
-  const idx = base.indexOf(marker);
-  if (idx === -1) return base;
+  // Direct layout: /.gsd/worktrees/
+  const directMarker = `${pathSep}.gsd${pathSep}worktrees${pathSep}`;
+  let idx = base.indexOf(directMarker);
+  if (idx === -1) {
+    // Symlink-resolved layout: /.gsd/projects/<hash>/worktrees/
+    const symlinkRe = new RegExp(
+      `\\${pathSep}\\.gsd\\${pathSep}projects\\${pathSep}[a-f0-9]+\\${pathSep}worktrees\\${pathSep}`,
+    );
+    const match = base.match(symlinkRe);
+    if (!match || match.index === undefined) return base;
+    idx = match.index;
+  }
 
   // base is inside .gsd/worktrees/<something> — extract the project root
   const projectRoot = base.slice(0, idx);

src/resources/extensions/gsd/captures.ts

@@ -59,8 +59,17 @@ const VALID_CLASSIFICATIONS: readonly string[] = [
  */
 export function resolveCapturesPath(basePath: string): string {
   const resolved = resolve(basePath);
+  // Direct layout: /.gsd/worktrees/
   const worktreeMarker = `${sep}.gsd${sep}worktrees${sep}`;
-  const idx = resolved.indexOf(worktreeMarker);
+  let idx = resolved.indexOf(worktreeMarker);
+  if (idx === -1) {
+    // Symlink-resolved layout: /.gsd/projects/<hash>/worktrees/
+    const symlinkRe = new RegExp(
+      `\\${sep}\\.gsd\\${sep}projects\\${sep}[a-f0-9]+\\${sep}worktrees\\${sep}`,
+    );
+    const match = resolved.match(symlinkRe);
+    if (match && match.index !== undefined) idx = match.index;
+  }
   if (idx !== -1) {
     // basePath is inside a worktree — resolve to project root
     const projectRoot = resolved.slice(0, idx);

src/resources/extensions/gsd/tests/worktree.test.ts

@@ -11,6 +11,7 @@ import {
   getMainBranch,
   getSliceBranchName,
   parseSliceBranch,
+  resolveProjectRoot,
   setActiveMilestoneId,
   SLICE_BRANCH_RE,
 } from "../worktree.ts";
@@ -165,6 +166,52 @@ async function main(): Promise<void> {
     rmSync(repo, { recursive: true, force: true });
   }
 
+  // ── detectWorktreeName: symlink-resolved paths ───────────────────────────
+  console.log("\n=== detectWorktreeName (symlink-resolved paths) ===");
+  assertEq(
+    detectWorktreeName("/Users/fran/.gsd/projects/89e1c9ad49bf/worktrees/M001"),
+    "M001",
+    "detects milestone in symlink-resolved path",
+  );
+  assertEq(
+    detectWorktreeName("/Users/fran/.gsd/projects/abc123/worktrees/M002/subdir"),
+    "M002",
+    "detects milestone with trailing subdir in symlink-resolved path",
+  );
+  assertEq(
+    detectWorktreeName("/Users/fran/.gsd/projects/abc123"),
+    null,
+    "returns null for project root without worktrees segment",
+  );
+  assertEq(
+    detectWorktreeName("/foo/.gsd/worktrees/M001"),
+    "M001",
+    "still detects direct layout path",
+  );
+
+  // ── resolveProjectRoot: symlink-resolved paths ──────────────────────────
+  console.log("\n=== resolveProjectRoot (symlink-resolved paths) ===");
+  assertEq(
+    resolveProjectRoot("/Users/fran/.gsd/projects/89e1c9ad49bf/worktrees/M001"),
+    "/Users/fran",
+    "resolves to user home for symlink-resolved path",
+  );
+  assertEq(
+    resolveProjectRoot("/foo/.gsd/worktrees/M001"),
+    "/foo",
+    "still resolves direct layout path",
+  );
+  assertEq(
+    resolveProjectRoot("/some/repo"),
+    "/some/repo",
+    "returns unchanged for non-worktree path",
+  );
+  assertEq(
+    resolveProjectRoot("/data/.gsd/projects/deadbeef/worktrees/M003/nested"),
+    "/data",
+    "resolves correctly with nested subdirs after worktree name",
+  );
+
   rmSync(base, { recursive: true, force: true });
   report();
 }

src/resources/extensions/gsd/worktree.ts

@@ -67,40 +67,60 @@ export function captureIntegrationBranch(basePath: string, milestoneId: string,
 
 // ─── Pure Utility Functions (unchanged) ────────────────────────────────────
 
+/**
+ * Find the worktrees segment in a path, supporting both direct
+ * (`/.gsd/worktrees/`) and symlink-resolved (`/.gsd/projects/<hash>/worktrees/`)
+ * layouts.  When `.gsd` is a symlink to `~/.gsd/projects/<hash>`, resolved
+ * paths contain the intermediate `projects/<hash>/` segment that the old
+ * single-marker check missed.
+ */
+function findWorktreeSegment(normalizedPath: string): { gsdIdx: number; afterWorktrees: number } | null {
+  // Direct layout: /.gsd/worktrees/<name>
+  const directMarker = "/.gsd/worktrees/";
+  const idx = normalizedPath.indexOf(directMarker);
+  if (idx !== -1) {
+    return { gsdIdx: idx, afterWorktrees: idx + directMarker.length };
+  }
+  // Symlink-resolved layout: /.gsd/projects/<hash>/worktrees/<name>
+  const symlinkRe = /\/\.gsd\/projects\/[a-f0-9]+\/worktrees\//;
+  const match = normalizedPath.match(symlinkRe);
+  if (match && match.index !== undefined) {
+    return { gsdIdx: match.index, afterWorktrees: match.index + match[0].length };
+  }
+  return null;
+}
+
 /**
  * Detect the active worktree name from the current working directory.
  * Returns null if not inside a GSD worktree (.gsd/worktrees/<name>/).
  */
 export function detectWorktreeName(basePath: string): string | null {
   const normalizedPath = basePath.replaceAll("\\", "/");
-  const marker = "/.gsd/worktrees/";
-  const idx = normalizedPath.indexOf(marker);
-  if (idx === -1) return null;
-  const afterMarker = normalizedPath.slice(idx + marker.length);
+  const seg = findWorktreeSegment(normalizedPath);
+  if (!seg) return null;
+  const afterMarker = normalizedPath.slice(seg.afterWorktrees);
   const name = afterMarker.split("/")[0];
   return name || null;
 }
 
 /**
  * Resolve the project root from a path that may be inside a worktree.
- * If the path contains `/.gsd/worktrees/<name>/`, returns the portion
- * before `/.gsd/`. Otherwise returns the input unchanged.
+ * If the path contains a worktrees segment, returns the portion before
+ * `/.gsd/`. Otherwise returns the input unchanged.
  *
  * Use this in commands that call `process.cwd()` to ensure they always
  * operate against the real project root, not a worktree subdirectory.
  */
 export function resolveProjectRoot(basePath: string): string {
   const normalizedPath = basePath.replaceAll("\\", "/");
-  const marker = "/.gsd/worktrees/";
-  const idx = normalizedPath.indexOf(marker);
-  if (idx === -1) return basePath;
-  // Return the original path up to the .gsd/ marker (un-normalized)
-  // Account for potential OS-specific separators
+  const seg = findWorktreeSegment(normalizedPath);
+  if (!seg) return basePath;
+  // Return the original path up to the /.gsd/ boundary
   const sep = basePath.includes("\\") ? "\\" : "/";
-  const markerOs = `${sep}.gsd${sep}worktrees${sep}`;
-  const idxOs = basePath.indexOf(markerOs);
-  if (idxOs !== -1) return basePath.slice(0, idxOs);
-  return basePath.slice(0, idx);
+  const gsdMarker = `${sep}.gsd${sep}`;
+  const gsdIdx = basePath.indexOf(gsdMarker);
+  if (gsdIdx !== -1) return basePath.slice(0, gsdIdx);
+  return basePath.slice(0, seg.gsdIdx);
 }
 
 /**