@opengsd/gsd-pi 1.3.0 → 1.4.0-dev.5fc22c6f

package/src/resources/extensions/gsd/worktree-manager.ts

@@ -19,7 +19,7 @@
  *   4. remove()  — git worktree remove + branch cleanup
  */
 
-import { existsSync, lstatSync, mkdirSync, readdirSync, readFileSync, realpathSync, rmSync, statSync } from "node:fs";
+import { cpSync, existsSync, lstatSync, mkdirSync, readdirSync, readFileSync, realpathSync, renameSync, rmSync, statSync, unlinkSync, writeFileSync } from "node:fs";
 import { execFileSync } from "node:child_process";
 import { join, resolve, sep } from "node:path";
 import { GSDError, GSD_PARSE_ERROR, GSD_STALE_STATE, GSD_LOCK_HELD, GSD_GIT_ERROR, GSD_MERGE_CONFLICT } from "./errors.js";
@@ -37,6 +37,7 @@ import {
   nativeGetCurrentBranch,
   nativeIsAncestor,
   nativeLogOneline,
+  nativeMergeAbort,
   nativeMergeSquash,
   nativeWorktreeAdd,
   nativeWorktreeList,
@@ -87,6 +88,34 @@ function deleteBranchIfPresent(basePath: string, branch: string, warningPrefix:
   }
 }
 
+function cleanupFailedSquashMergeState(basePath: string): void {
+  try {
+    nativeMergeAbort(basePath);
+  } catch (e) {
+    // Squash conflicts may not create MERGE_HEAD; this is expected.
+    logWarning("worktree", `merge abort skipped: ${(e as Error).message}`);
+  }
+  try {
+    execFileSync("git", ["reset", "--merge"], {
+      cwd: basePath,
+      stdio: ["ignore", "pipe", "pipe"],
+      encoding: "utf-8",
+    });
+  } catch (e) {
+    logWarning("worktree", `failed squash merge reset failed: ${(e as Error).message}`);
+  }
+
+  const gitDir = resolveGitDir(basePath);
+  for (const marker of ["SQUASH_MSG", "MERGE_MSG", "MERGE_MODE", "MERGE_HEAD", "AUTO_MERGE"]) {
+    try {
+      const markerPath = join(gitDir, marker);
+      if (existsSync(markerPath)) unlinkSync(markerPath);
+    } catch (e) {
+      logWarning("worktree", `failed squash merge marker cleanup failed (${marker}): ${(e as Error).message}`);
+    }
+  }
+}
+
 // ─── Path Helpers ──────────────────────────────────────────────────────────
 
 function normalizePathForComparison(path: string): string {
@@ -198,6 +227,113 @@ function isRegisteredGitWorktreeAtPath(basePath: string, wtPath: string): boolea
   }
 }
 
+function inspectUncommittedWorktreeState(wtPath: string): { dirty: boolean; status: string } {
+  try {
+    const status = execFileSync(
+      "git",
+      ["status", "--porcelain=v1", "--untracked-files=all"],
+      { cwd: wtPath, stdio: ["ignore", "pipe", "pipe"], encoding: "utf-8" },
+    ).trimEnd();
+    return { dirty: status.length > 0, status };
+  } catch (err) {
+    const message = err instanceof Error ? err.message : String(err);
+    logWarning(
+      "worktree",
+      `dirty worktree inspection failed for ${wtPath}: ${message}`,
+    );
+    // Fail closed: unknown state must quarantine rather than force-remove.
+    return { dirty: true, status: `git status failed: ${message}` };
+  }
+}
+
+function timestampForPath(): string {
+  return new Date().toISOString().replace(/[:.]/g, "-");
+}
+
+function uniqueQuarantinePath(basePath: string, name: string): string {
+  const root = join(basePath, ".gsd", "quarantine", "worktrees");
+  const baseName = `${name}-${timestampForPath()}`;
+  let candidate = join(root, baseName);
+  let suffix = 2;
+  while (existsSync(candidate)) {
+    candidate = join(root, `${baseName}-${suffix}`);
+    suffix++;
+  }
+  return candidate;
+}
+
+function quarantineDirtyWorktree(
+  basePath: string,
+  name: string,
+  branch: string,
+  wtPath: string,
+  status: string,
+): string | null {
+  const quarantinePath = uniqueQuarantinePath(basePath, name);
+  mkdirSync(join(basePath, ".gsd", "quarantine", "worktrees"), { recursive: true });
+
+  let moved = false;
+  try {
+    renameSync(wtPath, quarantinePath);
+    moved = true;
+  } catch (renameErr) {
+    logWarning(
+      "worktree",
+      `dirty worktree rename quarantine failed for ${name}: ${renameErr instanceof Error ? renameErr.message : String(renameErr)}; trying copy snapshot`,
+    );
+    try {
+      cpSync(wtPath, quarantinePath, { recursive: true, force: false, errorOnExist: true });
+    } catch (copyErr) {
+      logWarning(
+        "reconcile",
+        `Dirty worktree quarantine failed; preserving original worktree ${wtPath}: ${copyErr instanceof Error ? copyErr.message : String(copyErr)}`,
+        { worktree: name, path: wtPath },
+      );
+      return null;
+    }
+  }
+
+  try {
+    const gitFile = join(quarantinePath, ".git");
+    if (existsSync(gitFile) && lstatSync(gitFile).isFile()) {
+      unlinkSync(gitFile);
+    }
+  } catch (err) {
+    logWarning(
+      "worktree",
+      `failed to remove quarantined worktree git pointer: ${err instanceof Error ? err.message : String(err)}`,
+    );
+  }
+
+  try {
+    writeFileSync(
+      join(quarantinePath, ".gsd-quarantine.json"),
+      JSON.stringify({
+        kind: "dirty-worktree",
+        worktree: name,
+        branch,
+        originalPath: wtPath,
+        moved,
+        quarantinedAt: new Date().toISOString(),
+        status,
+      }, null, 2) + "\n",
+      "utf-8",
+    );
+  } catch (err) {
+    logWarning(
+      "worktree",
+      `failed to write worktree quarantine metadata: ${err instanceof Error ? err.message : String(err)}`,
+    );
+  }
+
+  logWarning(
+    "reconcile",
+    `Quarantined dirty worktree ${name} at ${quarantinePath} before removal. Branch ${branch} was preserved.`,
+    { worktree: name, path: quarantinePath, branch },
+  );
+  return quarantinePath;
+}
+
 /** True when `wtPath` has a git worktree checkout marker (`.git` file with gitdir pointer). */
 export function isLiveGitWorktreeCheckout(wtPath: string): boolean {
   const gitPath = join(wtPath, ".git");
@@ -287,7 +423,7 @@ export function pruneEphemeralGhostWorktreeDirectories(basePath: string): string
   return removed;
 }
 
-function removeStaleWorktreeDirectory(wtPath: string, name: string): void {
+export function removeStaleWorktreeDirectory(wtPath: string, name: string): void {
   logWarning(
     "reconcile",
     `Removing stale worktree directory (not registered with git): ${wtPath}`,
@@ -701,12 +837,13 @@ export function removeWorktree(
   basePath: string,
   name: string,
   opts: { deleteBranch?: boolean; force?: boolean; branch?: string } = {},
-): void {
+): boolean {
   basePath = normalizeBasePathForWorktreeOps(basePath);
 
   let wtPath = worktreePath(basePath, name);
   const branch = opts.branch ?? worktreeBranchName(name);
   const { deleteBranch = true, force = true } = opts;
+  let deleteBranchAfterRemoval = deleteBranch;
 
   // Resolve the ACTUAL worktree path from git's worktree list.
   // The computed path may differ when .gsd/ is (or was) a symlink to an
@@ -759,10 +896,10 @@ export function removeWorktree(
 
   if (!existsSync(wtPath)) {
     nativeWorktreePrune(basePath);
-    if (deleteBranch) {
+    if (deleteBranchAfterRemoval) {
       deleteBranchIfPresent(basePath, branch, "nativeBranchDelete failed");
     }
-    return;
+    return true;
   }
 
   // Submodule safety (#2337): detect submodules with uncommitted changes
@@ -844,6 +981,35 @@ export function removeWorktree(
     }
   }
 
+  // Dirty-worktree quarantine (#2365): once submodule (#2337) and nested-.git
+  // (#2616) rescue have run — they commit/clean the tree first — quarantine any
+  // uncommitted state that remains instead of force-deleting it. Gate on a live
+  // git checkout so a stale local directory left behind by state-sync (which
+  // has no `.git` file and is not a registered worktree) is removed normally
+  // rather than quarantined; otherwise its branch would never be deleted and
+  // the worktree would never be unregistered (#1852).
+  if (force && resolvedPathSafe && isLiveGitWorktreeCheckout(resolvedWtPath)) {
+    const dirtyState = inspectUncommittedWorktreeState(resolvedWtPath);
+    if (dirtyState.dirty) {
+      const quarantinePath = quarantineDirtyWorktree(
+        basePath,
+        name,
+        branch,
+        resolvedWtPath,
+        dirtyState.status,
+      );
+      if (!quarantinePath) {
+        return false;
+      }
+
+      deleteBranchAfterRemoval = false;
+      if (!existsSync(resolvedWtPath)) {
+        nativeWorktreePrune(basePath);
+        return true;
+      }
+    }
+  }
+
   // Remove worktree — only use force/rmSync when the path is safely contained
   if (resolvedPathSafe) {
     // Remove worktree: try non-force first when submodules have changes,
@@ -894,9 +1060,10 @@ export function removeWorktree(
   // Prune stale entries so git knows the worktree is gone
   nativeWorktreePrune(basePath);
 
-  if (deleteBranch) {
+  if (deleteBranchAfterRemoval) {
     deleteBranchIfPresent(basePath, branch, "final branch delete failed");
   }
+  return true;
 }
 
 /**
@@ -964,11 +1131,11 @@ function parseDiffNameStatus(entries: { status: string; path: string }[]): Workt
  * Diff the .gsd/ directory between the worktree branch and main branch.
  * Returns a summary of added, modified, and removed GSD artifacts.
  */
-export function diffWorktreeGSD(basePath: string, name: string): WorktreeDiffSummary {
+export function diffWorktreeGSD(basePath: string, name: string, mainBranchOverride?: string): WorktreeDiffSummary {
   basePath = normalizeBasePathForWorktreeOps(basePath);
 
   const branch = worktreeBranchName(name);
-  const mainBranch = nativeDetectMainBranch(basePath);
+  const mainBranch = mainBranchOverride ?? nativeDetectMainBranch(basePath);
 
   const entries = nativeDiffNameStatus(basePath, mainBranch, branch, ".gsd/", true);
 
@@ -981,11 +1148,16 @@ export function diffWorktreeGSD(basePath: string, name: string): WorktreeDiffSum
  * on main when the merge is applied. If both branches have identical
  * content, this correctly returns an empty diff.
  */
-export function diffWorktreeAll(basePath: string, name: string, branchOverride?: string): WorktreeDiffSummary {
+export function diffWorktreeAll(
+  basePath: string,
+  name: string,
+  branchOverride?: string,
+  mainBranchOverride?: string,
+): WorktreeDiffSummary {
   basePath = normalizeBasePathForWorktreeOps(basePath);
 
   const branch = branchOverride ?? worktreeBranchName(name);
-  const mainBranch = nativeDetectMainBranch(basePath);
+  const mainBranch = mainBranchOverride ?? nativeDetectMainBranch(basePath);
 
   const entries = nativeDiffNameStatus(basePath, mainBranch, branch);
 
@@ -996,11 +1168,16 @@ export function diffWorktreeAll(basePath: string, name: string, branchOverride?:
  * Get per-file line addition/deletion stats for what will change on main.
  * Uses direct diff (not merge-base) so the preview matches the actual merge outcome.
  */
-export function diffWorktreeNumstat(basePath: string, name: string, branchOverride?: string): FileLineStat[] {
+export function diffWorktreeNumstat(
+  basePath: string,
+  name: string,
+  branchOverride?: string,
+  mainBranchOverride?: string,
+): FileLineStat[] {
   basePath = normalizeBasePathForWorktreeOps(basePath);
 
   const branch = branchOverride ?? worktreeBranchName(name);
-  const mainBranch = nativeDetectMainBranch(basePath);
+  const mainBranch = mainBranchOverride ?? nativeDetectMainBranch(basePath);
 
   const rawStats = nativeDiffNumstat(basePath, mainBranch, branch);
 
@@ -1016,11 +1193,11 @@ export function diffWorktreeNumstat(basePath: string, name: string, branchOverri
  * Get the full diff content for .gsd/ between the worktree branch and main.
  * Returns the raw unified diff for LLM consumption.
  */
-export function getWorktreeGSDDiff(basePath: string, name: string): string {
+export function getWorktreeGSDDiff(basePath: string, name: string, mainBranchOverride?: string): string {
   basePath = normalizeBasePathForWorktreeOps(basePath);
 
   const branch = worktreeBranchName(name);
-  const mainBranch = nativeDetectMainBranch(basePath);
+  const mainBranch = mainBranchOverride ?? nativeDetectMainBranch(basePath);
 
   return nativeDiffContent(basePath, mainBranch, branch, ".gsd/", undefined, true);
 }
@@ -1029,11 +1206,11 @@ export function getWorktreeGSDDiff(basePath: string, name: string): string {
  * Get the full diff content for non-.gsd/ files between the worktree branch and main.
  * Returns the raw unified diff for LLM consumption.
  */
-export function getWorktreeCodeDiff(basePath: string, name: string): string {
+export function getWorktreeCodeDiff(basePath: string, name: string, mainBranchOverride?: string): string {
   basePath = normalizeBasePathForWorktreeOps(basePath);
 
   const branch = worktreeBranchName(name);
-  const mainBranch = nativeDetectMainBranch(basePath);
+  const mainBranch = mainBranchOverride ?? nativeDetectMainBranch(basePath);
 
   return nativeDiffContent(basePath, mainBranch, branch, undefined, ".gsd/", true);
 }
@@ -1041,11 +1218,11 @@ export function getWorktreeCodeDiff(basePath: string, name: string): string {
 /**
  * Get commit log for the worktree branch since it diverged from main.
  */
-export function getWorktreeLog(basePath: string, name: string): string {
+export function getWorktreeLog(basePath: string, name: string, mainBranchOverride?: string): string {
   basePath = normalizeBasePathForWorktreeOps(basePath);
 
   const branch = worktreeBranchName(name);
-  const mainBranch = nativeDetectMainBranch(basePath);
+  const mainBranch = mainBranchOverride ?? nativeDetectMainBranch(basePath);
 
   const entries = nativeLogOneline(basePath, mainBranch, branch);
 
@@ -1057,11 +1234,17 @@ export function getWorktreeLog(basePath: string, name: string): string {
  * Must be called from the main working tree (not the worktree itself).
  * Returns the merge commit message.
  */
-export function mergeWorktreeToMain(basePath: string, name: string, commitMessage: string, branchOverride?: string): string {
+export function mergeWorktreeToMain(
+  basePath: string,
+  name: string,
+  commitMessage: string,
+  branchOverride?: string,
+  mainBranchOverride?: string,
+): string {
   basePath = normalizeBasePathForWorktreeOps(basePath);
 
   const branch = branchOverride ?? worktreeBranchName(name);
-  const mainBranch = nativeDetectMainBranch(basePath);
+  const mainBranch = mainBranchOverride ?? nativeDetectMainBranch(basePath);
   const current = nativeGetCurrentBranch(basePath);
 
   if (current !== mainBranch) {
@@ -1070,6 +1253,17 @@ export function mergeWorktreeToMain(basePath: string, name: string, commitMessag
 
   const result = nativeMergeSquash(basePath, branch);
   if (!result.success) {
+    const dirtyWorkingTree = result.conflicts.includes("__dirty_working_tree__");
+    if (!dirtyWorkingTree) {
+      cleanupFailedSquashMergeState(basePath);
+    }
+    if (!dirtyWorkingTree && branch.startsWith("milestone/")) {
+      try {
+        removeWorktree(basePath, name, { branch, deleteBranch: true, force: true });
+      } catch (e) {
+        logWarning("worktree", `failed milestone branch cleanup after squash merge failure: ${(e as Error).message}`);
+      }
+    }
     throw new GSDError(GSD_MERGE_CONFLICT, `Merge conflicts detected in: ${result.conflicts.join(", ")}`);
   }
 

package/src/resources/extensions/gsd/worktree-safety.ts

@@ -7,7 +7,7 @@ import { join, resolve } from "node:path";
 
 import { normalizeWorktreePathForCompare } from "./worktree-root.js";
 import { worktreesDirs } from "./worktree-placement.js";
-import { listWorktrees } from "./worktree-manager.js";
+import { listWorktrees, removeStaleWorktreeDirectory } from "./worktree-manager.js";
 import { getCurrentBranch } from "./worktree.js";
 
 export type WorktreeSafetyWriteScope = "planning-only" | "source-writing";
@@ -74,6 +74,7 @@ export interface WorktreeSafetyDeps {
   lstatSync(path: string): Pick<Stats, "isFile">;
   listRegisteredWorktrees?(projectRoot: string): readonly RegisteredWorktree[];
   pruneRegisteredWorktrees?(projectRoot: string): void;
+  removeStaleWorktreeDirectory?(unitRoot: string, milestoneId: string): void;
   getCurrentBranch?(unitRoot: string): string;
 }
 
@@ -100,6 +101,7 @@ const defaultDeps: WorktreeSafetyDeps = {
       stdio: "pipe",
     });
   },
+  removeStaleWorktreeDirectory,
   getCurrentBranch,
 };
 
@@ -127,8 +129,6 @@ function errorMessage(error: unknown): string {
 export function createWorktreeSafetyModule(
   deps: WorktreeSafetyDeps = defaultDeps,
 ): WorktreeSafetyModule {
-  const unregisteredRecoveryFailed = new Set<string>();
-
   return {
     validateUnitRoot(input) {
       if (input.writeScope === "planning-only") {
@@ -230,22 +230,17 @@ export function createWorktreeSafetyModule(
           );
         }
         if (registered && !registered.some((worktree) => samePath(worktree.path, unitRoot))) {
-          const wasPreviouslyTracked = unregisteredRecoveryFailed.has(unitRoot);
           let attemptedPrune = false;
 
-          if (!wasPreviouslyTracked && deps.pruneRegisteredWorktrees) {
+          if (deps.pruneRegisteredWorktrees) {
             attemptedPrune = true;
             try {
               deps.pruneRegisteredWorktrees(projectRoot);
               const rechecked = deps.listRegisteredWorktrees?.(projectRoot);
               if (rechecked?.some((worktree) => samePath(worktree.path, unitRoot))) {
-                unregisteredRecoveryFailed.delete(unitRoot);
                 registered = rechecked;
-              } else {
-                unregisteredRecoveryFailed.add(unitRoot);
               }
             } catch (error) {
-              unregisteredRecoveryFailed.add(unitRoot);
               return failure(
                 "worktree-git-probe-failed",
                 `Unable to recover unregistered worktree root ${unitRoot}.`,
@@ -256,13 +251,38 @@ export function createWorktreeSafetyModule(
           }
 
           if (!registered?.some((worktree) => samePath(worktree.path, unitRoot))) {
+            // The directory exists on disk with a .git marker but git no longer
+            // tracks it as a worktree (e.g. a prior removeWorktree crash left the
+            // directory while `git worktree prune` cleaned the registry). Remove
+            // the orphaned directory — the same cleanup createWorktree performs —
+            // so the next dispatch recreates the milestone worktree from scratch
+            // instead of looping forever on worktree-unregistered (#803, #590).
+            if (deps.removeStaleWorktreeDirectory) {
+              try {
+                deps.removeStaleWorktreeDirectory(unitRoot, milestoneId);
+                return failure(
+                  "worktree-missing",
+                  `Worktree root ${unitRoot} was not registered with git; removed the orphaned directory so it can be recreated.`,
+                  "Recreate the milestone worktree before dispatching the source-writing Unit. Auto-mode recreates it automatically on the next dispatch.",
+                  { unitRoot, attemptedPrune, removedStaleDirectory: true },
+                );
+              } catch (error) {
+                return failure(
+                  "worktree-unregistered",
+                  `Worktree root ${unitRoot} is not registered with git worktree list and the orphaned directory could not be removed.`,
+                  "Remove the orphaned worktree directory manually (it may be locked by another process), then recreate or re-register the milestone worktree before dispatching the source-writing Unit.",
+                  { unitRoot, attemptedPrune, removedStaleDirectory: false, error: errorMessage(error) },
+                );
+              }
+            }
+
             return failure(
               "worktree-unregistered",
               `Worktree root ${unitRoot} is not registered with git worktree list.`,
-              attemptedPrune || wasPreviouslyTracked
+              attemptedPrune
                 ? "Worktree recovery was attempted but the root is still unregistered. Recreate or re-register the milestone worktree before dispatching the source-writing Unit."
                 : "Run 'git worktree prune'. If still unregistered, recreate or re-register the milestone worktree before dispatching the source-writing Unit.",
-              { unitRoot, attemptedPrune, trackedAsFailed: unregisteredRecoveryFailed.has(unitRoot) },
+              { unitRoot, attemptedPrune },
             );
           }
         }

package/src/resources/extensions/mcp-client/manager.ts

@@ -490,7 +490,7 @@ function normalizeRawServerConfig(
 		cwd: typeof config.cwd === "string" ? config.cwd : undefined,
 		headers,
 		oauth: config.oauth && typeof config.oauth === "object" ? config.oauth as McpHttpAuthConfig["oauth"] : undefined,
-		envWarnings: collectEnvWarnings([
+		envWarnings: collectMcpEnvWarnings([
 			["url", url],
 			...Object.entries(env ?? {}).map(([key, value]) => [`env.${key}`, value] as [string, string | undefined]),
 			...Object.entries(headers ?? {}).map(([key, value]) => [`headers.${key}`, value] as [string, string | undefined]),
@@ -498,7 +498,7 @@ function normalizeRawServerConfig(
 	};
 }
 
-function detectTransport(config: Record<string, unknown>): ManagedMcpTransport {
+export function detectTransport(config: Record<string, unknown>): ManagedMcpTransport {
 	const type = typeof config.type === "string" ? config.type.toLowerCase() : undefined;
 	if (type && type !== "stdio" && type !== "http") return "unsupported";
 	if (typeof config.command === "string") return "stdio";
@@ -530,7 +530,7 @@ function serializeServerInput(input: ManagedMcpServerInput): Record<string, unkn
 	});
 }
 
-function collectEnvWarnings(values: Array<[string, string | undefined]>): string[] {
+export function collectMcpEnvWarnings(values: Array<[string, string | undefined]>): string[] {
 	const warnings: string[] = [];
 	for (const [label, value] of values) {
 		if (!value) continue;

package/dist/web/standalone/.next/static/chunks/2772.bfa657f49f955239.js

@@ -1 +0,0 @@
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