@opengsd/gsd-pi 1.0.2-dev.e70300c → 1.0.2-dev.fb7ddf1

package/dist/resources/extensions/gsd/parallel-merge.js

@@ -117,18 +117,20 @@ export async function mergeCompletedMilestone(basePath, milestoneId) {
     // to read it from. Only use the worktree path when git actually knows
     // about it (`getAutoWorktreePath` returns non-null). When the directory
     // exists on disk but isn't a registered git worktree (e.g. a stale
-    // session-status marker dir), fall back to the project root and let the
-    // standalone's mode detection pick branch-mode or skipped — using the
-    // un-registered dir as `worktreeBasePath` would cause `getCurrentBranch`
-    // to fail with a "Worktree HEAD diverged" error.
+    // session-status marker dir), recover through branch mode from the project
+    // root. Letting worktree-mode run from the project root can auto-commit
+    // overlapping root files to the integration branch before the squash merge,
+    // creating a synthetic conflict.
     const registeredWtPath = getAutoWorktreePath(basePath, milestoneId);
     const worktreeBasePath = registeredWtPath ?? basePath;
+    const isolationModeOverride = registeredWtPath ? undefined : "branch";
     let result;
     try {
         result = mergeMilestoneStandalone(buildWorktreeLifecycleDeps(), {
             originalBasePath: basePath,
             worktreeBasePath,
             milestoneId,
+            isolationModeOverride,
             // Parallel context never runs with degraded isolation — workers only
             // exist when isolation succeeded. Pass `false` explicitly so the
             // standalone's degraded-skip branch is not reached.

package/dist/resources/extensions/gsd/parallel-monitor-overlay.js

@@ -7,7 +7,7 @@ import { matchesKey, Key } from "@gsd/pi-tui";
 import { formatDuration } from "../shared/mod.js";
 import { formattedShortcutPair } from "./shortcut-defs.js";
 import { resolveGsdPathContract } from "./paths.js";
-import { renderBar, renderKeyHints, renderProgressBar, safeLine, statusGlyph, } from "./tui/render-kit.js";
+import { renderBar, renderDialogFrame, renderKeyHints, renderProgressBar, safeLine, statusGlyph, } from "./tui/render-kit.js";
 // ─── Data Helpers ─────────────────────────────────────────────────────────
 function readJsonSafe(filePath) {
     try {
@@ -306,15 +306,14 @@ export class ParallelMonitorOverlay {
         const t = this.theme;
         const lines = [];
         const w = Math.max(1, width);
-        // Header
+        const contentWidth = Math.max(1, w - 4);
         const totalCost = this.workers.reduce((s, wk) => s + wk.cost, 0);
         const aliveCount = this.workers.filter((wk) => wk.alive).length;
         const now = new Date().toLocaleTimeString();
-        lines.push(t.bold(t.fg("accent", " GSD Parallel Monitor ")));
         lines.push(t.fg("muted", `  ${now}  │  ${aliveCount}/${this.workers.length} alive  │  Total: `) +
             t.bold(`$${totalCost.toFixed(2)}`) +
             t.fg("muted", "  │  5s refresh"));
-        lines.push(renderBar(t, w));
+        lines.push(renderBar(t, contentWidth));
         if (this.workers.length === 0) {
             lines.push("");
             lines.push(t.fg("warning", "  No parallel workers found."));
@@ -360,7 +359,7 @@ export class ParallelMonitorOverlay {
                     });
                     lines.push(`     ${t.fg("muted", "slices")}  ${chips.join("  ")}`);
                     // Task progress bar
-                    const barWidth = Math.max(6, Math.min(25, w - 32));
+                    const barWidth = Math.max(6, Math.min(25, contentWidth - 32));
                     const bar = renderProgressBar(t, wk.doneTasks, wk.totalTasks, barWidth, {
                         filledChar: "█",
                         emptyChar: "░",
@@ -378,7 +377,7 @@ export class ParallelMonitorOverlay {
         }
         // Event feed
         lines.push("");
-        lines.push(renderBar(t, w));
+        lines.push(renderBar(t, contentWidth));
         lines.push(`  ${t.bold("Recent Events")}`);
         if (this.events.length === 0) {
             lines.push(t.fg("muted", "  No events yet..."));
@@ -389,7 +388,6 @@ export class ParallelMonitorOverlay {
                 lines.push(`  ${t.fg("muted", "│")} ${t.fg("accent", mid)} ${evt.replace(/^✓ M\d+\//, "")}`);
             }
         }
-        // Footer
         lines.push("");
         const allDone = this.workers.length > 0 && this.workers.every((wk) => !wk.alive);
         if (allDone) {
@@ -400,16 +398,20 @@ export class ParallelMonitorOverlay {
             }
             lines.push(`  ${t.bold("Total: $" + this.workers.reduce((s, wk) => s + wk.cost, 0).toFixed(2))}`);
         }
-        lines.push(renderKeyHints(t, [`ESC/q/${formattedShortcutPair("parallel")} close`, "↑↓ scroll"], w));
         // Apply scroll — use terminal rows as height estimate
         const termHeight = process.stdout.rows || 40;
-        const maxScroll = Math.max(0, lines.length - termHeight);
+        const maxBodyRows = Math.max(1, Math.min(lines.length, termHeight - 12));
+        const maxScroll = Math.max(0, lines.length - maxBodyRows);
         this.scrollOffset = Math.min(Math.max(this.scrollOffset, 0), maxScroll);
         const visible = lines
-            .slice(this.scrollOffset, this.scrollOffset + termHeight)
-            .map((line) => safeLine(line, w));
-        this.cachedLines = visible;
+            .slice(this.scrollOffset, this.scrollOffset + maxBodyRows)
+            .map((line) => safeLine(line, contentWidth));
+        const footer = renderKeyHints(t, [`ESC/q/${formattedShortcutPair("parallel")} close`, "↑↓ scroll"], contentWidth);
+        this.cachedLines = renderDialogFrame(t, "GSD Parallel Monitor", visible, w, {
+            footer,
+            scroll: { offset: this.scrollOffset, visibleRows: maxBodyRows, totalRows: lines.length },
+        });
         this.cachedWidth = width;
-        return visible;
+        return this.cachedLines;
     }
 }

package/dist/resources/extensions/gsd/post-execution-checks.js

@@ -242,10 +242,11 @@ export function checkImportResolution(taskRow, _priorTasks, basePath) {
         }
         const imports = extractRelativeImports(source);
         for (const { importPath, lineNum } of imports) {
-            // React Router generated +types modules may not exist on disk during
-            // post-exec checks (generated during framework build). Don't block task
-            // completion on these imports.
-            if (/^\.{1,2}\/\+types\//.test(importPath)) {
+            // Framework-generated type modules may not exist on disk during post-exec
+            // checks (typically generated during framework builds/typegen). Don't
+            // block task completion on these imports.
+            if (/^\.{1,2}\/\+types\//.test(importPath) ||
+                /^(?:\.{1,2}\/)+(?:[^/]+\/)*\$types(?:$|\/)/.test(importPath)) {
                 continue;
             }
             const resolution = resolveImportPath(importPath, file, basePath);

package/dist/resources/extensions/gsd/preferences-skills.js

@@ -11,10 +11,17 @@ import { gsdHome } from "./gsd-home.js";
 import { statSync } from "node:fs";
 import { validatePreferences } from "./preferences-validation.js";
 /**
- * Known skill directories, in priority order.
- * GSD bundled skills live in ~/.gsd/agent/skills/ and win name collisions.
- * User-global and project-local ecosystem directories remain available as
- * read-only discovery sources, followed by Claude Code compatibility paths.
+ * Known skill directories for **preference reference resolution** (bare skill names).
+ *
+ * Search order (first match wins):
+ * 1. ~/.gsd/agent/skills/ (GSD bundled)
+ * 2. ~/.agents/skills/ (ecosystem global)
+ * 3. .agents/skills/ (project ecosystem)
+ * 4. ~/.claude/skills/ and .claude/skills/ (Claude Code compatibility)
+ *
+ * Note: the ResourceLoader catalog uses PackageManager precedence instead —
+ * project `.gsd/skills` and `.agents/skills` can override bundled GSD skills
+ * on name collision. See docs/dev/what-is-pi/09-the-customization-stack.md.
  */
 export function getSkillSearchDirs(cwd) {
     const dirs = [

package/dist/resources/extensions/gsd/preferences.js

@@ -455,9 +455,10 @@ function mergePreDispatchHooks(base, override) {
     return merged.length > 0 ? merged : undefined;
 }
 // ─── System Prompt Rendering ──────────────────────────────────────────────────
-export function renderPreferencesForSystemPrompt(preferences, resolutions) {
+export function renderPreferencesForSystemPrompt(preferences, resolutions, options) {
     const validated = validatePreferences(preferences);
     const lines = ["## GSD Skill Preferences"];
+    const includeResolvedPaths = options?.includeResolvedPaths ?? true;
     if (validated.errors.length > 0) {
         lines.push("- Validation: some preference values were ignored because they were invalid.");
     }
@@ -466,7 +467,18 @@ export function renderPreferencesForSystemPrompt(preferences, resolutions) {
     }
     preferences = validated.preferences;
     lines.push("- Treat these as explicit skill-selection policy for GSD work.", "- If a listed skill exists and is relevant, load and follow it instead of treating it as a vague suggestion.", "- Current user instructions still override these defaults.");
-    const fmt = (ref) => resolutions ? formatSkillRef(ref, resolutions) : ref;
+    const fmt = (ref) => {
+        if (!resolutions)
+            return ref;
+        if (!includeResolvedPaths) {
+            const resolution = resolutions.get(ref);
+            if (!resolution || resolution.method === "unresolved") {
+                return `${ref} (⚠ not found — check skill name or path)`;
+            }
+            return ref;
+        }
+        return formatSkillRef(ref, resolutions);
+    };
     if (preferences.always_use_skills && preferences.always_use_skills.length > 0) {
         lines.push("- Always use these skills when relevant:");
         for (const skill of preferences.always_use_skills) {

package/dist/resources/extensions/gsd/prompt-loader.js

@@ -21,6 +21,7 @@ import { join, dirname } from "node:path";
 import { fileURLToPath } from "node:url";
 import { logWarning } from "./workflow-logger.js";
 import { gsdHome } from "./gsd-home.js";
+import { chooseVisionAskVariant } from "./vision-ask.js";
 function hasRequiredExtensionAssets(rootDir, exists = existsSync) {
     return (exists(join(rootDir, "prompts")) &&
         exists(join(rootDir, "templates", "task-summary.md")));
@@ -168,6 +169,7 @@ export function loadPrompt(name, vars = {}) {
         planTemplatePath: join(getTemplatesDir(), "plan.md"),
         taskPlanTemplatePath: join(getTemplatesDir(), "task-plan.md"),
         taskSummaryTemplatePath: join(getTemplatesDir(), "task-summary.md"),
+        visionAsk: chooseVisionAskVariant(),
         skillActivation: "If a `GSD Skill Preferences` block is present in system context, use it and the `<available_skills>` catalog in your system prompt to decide which skills to load and follow for this unit, without relaxing required verification or artifact rules.",
         ...vars,
     };

package/dist/resources/extensions/gsd/prompts/discuss.md

@@ -1,8 +1,10 @@
 {{preamble}}
 
-Ask: "What's the vision?" once, then use the reply as vision input.
+Ask exactly this once: "{{visionAsk}}" Then use the user's reply as vision input.
 
-**Special handling:** If the **user's** message is status, branch state, clarification, or any other non-project-description, treat it as vision input and proceed instead of repeating "What's the vision?" Do **not** treat the system preamble above (e.g. "New milestone M00X.") as vision input — wait for the user.
+The opener is intentionally variable so GSD feels alive across project starts. Keep it natural, easy to answer, and assistant/developer shaped: plain language, light guidance, no corporate wording, no roleplay.
+
+**Special handling:** If the **user's** message is status, branch state, clarification, or any other non-project-description, treat it as vision input and proceed instead of repeating the opener. Do **not** treat the system preamble above (e.g. "New milestone M00X.") as vision input — wait for the user.
 
 ## Reflection Step
 

package/dist/resources/extensions/gsd/prompts/gate-evaluate.md

@@ -35,7 +35,7 @@ You are evaluating **quality gates in parallel** for this slice. Each gate is an
 2. **Wait for all subagents** to complete.
 3. **Verify each gate wrote its result** by checking that `gsd_save_gate_result` was called for each gate ID.
    - Call it **directly** — do **not** use `ToolSearch` (it is not available in GSD).
-   - Inside Claude Code use `mcp__gsd-workflow__gsd_save_gate_result`; otherwise use `gsd_save_gate_result`.
+   - Inside Claude Code use the active MCP-scoped workflow name for `gsd_save_gate_result`; otherwise use `gsd_save_gate_result`.
    - Always pass all required fields (camelCase): `milestoneId`, `sliceId`, `gateId`, `verdict`, `rationale`. Never call with an empty `{}` object.
 4. **Report the batch outcome** — which gates passed, which flagged concerns, and which were omitted as not applicable.
 

package/dist/resources/extensions/gsd/prompts/guided-discuss-milestone.md

@@ -4,6 +4,8 @@ Discuss milestone {{milestoneId}} ("{{milestoneTitle}}"). Identify real gray are
 
 **Structured questions available: {{structuredQuestionsAvailable}}**
 
+**Conversation opener:** For the first user-facing question round, if you need a broad starting question, use: "{{visionAsk}}" Pair it with investigation-shaped follow-ups. Keep the tone natural and easy to answer, like an assistant/developer helping the user shape the next piece of work.
+
 {{inlinedTemplates}}
 
 ---

package/dist/resources/extensions/gsd/prompts/system.md

@@ -19,9 +19,7 @@ Leave the project ready for the next agent to understand and continue. Artifacts
 
 ## Skills
 
-GSD ships with bundled skills. When the task matches, load the relevant skill file with `read` before starting. Use bare skill names; GSD resolves paths.
-
-{{bundledSkillsTable}}
+GSD ships with bundled skills. Installed skills are listed in `<available_skills>` in your system prompt — load the relevant skill file with `read` using the path shown there before starting matching work. Use bare skill names in preferences; GSD resolves paths.
 
 ## Hard Rules
 
@@ -122,18 +120,7 @@ Templates are in `{{templatesDir}}`.
 
 **Browser verification:** Verify frontend work against a running app. Discovery: `browser_find`/`browser_snapshot_refs`. Action: refs/selectors -> `browser_batch`. Verification: `browser_assert`. Diagnostics: `browser_diff` -> console/network logs -> full inspection as last resort. Retry only with a new hypothesis.
 
-### Anti-patterns — never do these
-
-- Never use `cat` to read a file you might edit; use `read`.
-- Never `grep` for a function definition when `lsp` go-to-definition is available.
-- Never poll servers with `sleep` loops; use `bg_shell wait_for_ready`.
-- Never background with `bash` + `&`; use `bg_shell start`.
-- Never use `bg_shell output` for status; use `digest`.
-- Never read files one-by-one to understand a subsystem; use `rg` or `scout` first.
-- Never guess library APIs; use `get_library_docs`.
-- Never ask the user to run/check/set something you can do.
-- Never await stale async jobs after editing source; cancel then re-run.
-- Never query `.gsd/gsd.db` directly via `sqlite3`, `better-sqlite3`, or `node -e require('better-sqlite3')`; the engine owns a single-writer WAL connection. Use `gsd_milestone_status`, `gsd_journal_query`, or other `gsd_*` tools.
+**Database:** Never query `.gsd/gsd.db` directly via `sqlite3`, `better-sqlite3`, or `node -e require('better-sqlite3')`; the engine owns a single-writer WAL connection. Use `gsd_milestone_status`, `gsd_journal_query`, or other `gsd_*` tools.
 
 ### Ask vs infer
 
@@ -173,8 +160,4 @@ Fix root causes, not symptoms. If applying temporary mitigation, label it and pr
 - When debugging, stay curious. Problems are puzzles. Say what's interesting about the failure before reaching for fixes.
 - After completing a task, give a brief summary and 2-4 numbered next-step options; last option is always "Other". Omit the list for strict output formats.
 
-Good narration: "Three existing handlers follow a middleware pattern - using that instead of a custom wrapper."
-Good narration: "Tests pass. Running slice-level verification."
-Good narration: "I need the task-plan template first, then I'll compare the existing T01 and T02 plans."
-Bad narration: "Reading the file now." / "Let me check this." / "I'll look at the tests next."
-Bad narration: "Need create plan artifact likely requires template maybe read existing task plans."
+Good narration states a decision or finding: "Three handlers follow a middleware pattern - using that instead of a custom wrapper." Bad narration just announces the next call ("Reading the file now.") or emits compressed planner notes ("Need create plan artifact maybe read existing plans.").

package/dist/resources/extensions/gsd/queue-reorder-ui.js

@@ -8,9 +8,9 @@
  * Conflicting depends_on entries are auto-removed on confirm.
  */
 import { Key, matchesKey, truncateToWidth } from "@gsd/pi-tui";
-import { makeUI } from "../shared/tui.js";
 import { GLYPH } from "../shared/mod.js";
 import { validateQueueOrder } from "./queue-order.js";
+import { renderDialogFrame, renderKeyHints } from "./tui/render-kit.js";
 /**
  * Show the queue reorder overlay.
  * Returns the new order + deps to remove, or null if cancelled.
@@ -26,6 +26,7 @@ export async function showQueueReorder(ctx, completed, pending) {
         let grabbed = false;
         let scrollOffset = 0;
         let cachedLines;
+        let cachedWidth;
         let validation;
         // Mutable deps map — tracks removals during this session
         const liveDeps = new Map();
@@ -42,6 +43,7 @@ export async function showQueueReorder(ctx, completed, pending) {
         revalidate();
         function refresh() {
             cachedLines = undefined;
+            cachedWidth = undefined;
             tui.requestRender();
         }
         function swapItems(fromIdx, toIdx) {
@@ -125,17 +127,14 @@ export async function showQueueReorder(ctx, completed, pending) {
             }
         }
         function render(width) {
-            if (cachedLines)
+            if (cachedLines && cachedWidth === width)
                 return cachedLines;
-            const ui = makeUI(theme, width);
+            const contentWidth = Math.max(1, width - 4);
             const lines = [];
             const queueRows = [];
-            const push = (...rows) => { for (const r of rows)
-                lines.push(...r); };
-            const add = (s) => truncateToWidth(s, width);
+            const add = (s) => truncateToWidth(s, contentWidth);
             let cursorQueueRow = 0;
-            const headerText = grabbed ? "  Queue Reorder — Moving Item" : "  Queue Reorder";
-            push(ui.bar(), ui.blank(), ui.header(headerText), ui.blank());
+            const headerText = grabbed ? "Queue Reorder - Moving Item" : "Queue Reorder";
             // Completed milestones (dimmed)
             if (completed.length > 0) {
                 lines.push(add(theme.fg("dim", "  Completed:")));
@@ -143,7 +142,7 @@ export async function showQueueReorder(ctx, completed, pending) {
                     const label = m.title && m.title !== m.id ? `${m.id}  ${m.title}` : m.id;
                     lines.push(add(`    ${theme.fg("dim", `${GLYPH.statusDone} ${label}`)}`));
                 }
-                push(ui.blank());
+                lines.push("");
             }
             // Pending milestones
             const queueLabel = grabbed ? "  Queue (space to release, ↑/↓ to move):" : "  Queue (space to grab, ↑/↓ to navigate):";
@@ -190,7 +189,7 @@ export async function showQueueReorder(ctx, completed, pending) {
             // Removed deps feedback
             const trailingLines = [];
             if (removedDeps.length > 0) {
-                trailingLines.push(...ui.blank());
+                trailingLines.push("");
                 for (const r of removedDeps) {
                     trailingLines.push(add(`  ${theme.fg("success", `${GLYPH.statusDone} Removed: ${r.milestone} depends_on ${r.dep}`)}`));
                 }
@@ -198,10 +197,9 @@ export async function showQueueReorder(ctx, completed, pending) {
             // Circular warning
             const circ = validation.violations.find(v => v.type === 'circular');
             if (circ) {
-                trailingLines.push(...ui.blank());
+                trailingLines.push("");
                 trailingLines.push(add(`  ${theme.fg("error", `${GLYPH.statusWarning} ${circ.message}`)}`));
             }
-            trailingLines.push(...ui.blank());
             // Hints — context-sensitive based on grab state
             const hints = [];
             if (grabbed) {
@@ -221,9 +219,9 @@ export async function showQueueReorder(ctx, completed, pending) {
                 hints.push("enter ok");
             }
             hints.push("esc");
-            trailingLines.push(...ui.hints(hints), ...ui.bar());
             const maxOverlayRows = Math.max(10, process.stdout.rows ? Math.floor(process.stdout.rows * 0.8) : 24);
-            const availableQueueRows = Math.max(1, maxOverlayRows - lines.length - trailingLines.length);
+            const frameRows = 4;
+            const availableQueueRows = Math.max(1, maxOverlayRows - frameRows - lines.length - trailingLines.length);
             const maxScroll = Math.max(0, queueRows.length - availableQueueRows);
             if (cursorQueueRow < scrollOffset) {
                 scrollOffset = cursorQueueRow;
@@ -232,11 +230,23 @@ export async function showQueueReorder(ctx, completed, pending) {
                 scrollOffset = cursorQueueRow - availableQueueRows + 1;
             }
             scrollOffset = Math.min(Math.max(scrollOffset, 0), maxScroll);
-            lines.push(...queueRows.slice(scrollOffset, scrollOffset + availableQueueRows), ...trailingLines);
-            cachedLines = lines;
-            return lines;
+            const queueStartRow = lines.length;
+            const visibleQueueRows = queueRows.slice(scrollOffset, scrollOffset + availableQueueRows);
+            lines.push(...visibleQueueRows, ...trailingLines);
+            cachedLines = renderDialogFrame(theme, headerText, lines, width, {
+                footer: renderKeyHints(theme, hints, contentWidth),
+                scroll: {
+                    offset: scrollOffset,
+                    visibleRows: availableQueueRows,
+                    totalRows: queueRows.length,
+                    trackOffset: queueStartRow,
+                    trackRows: visibleQueueRows.length,
+                },
+            });
+            cachedWidth = width;
+            return cachedLines;
         }
-        return { render, invalidate: () => { cachedLines = undefined; }, handleInput };
+        return { render, invalidate: () => { cachedLines = undefined; cachedWidth = undefined; }, handleInput };
     }, {
         overlay: true,
         overlayOptions: { width: "70%", minWidth: 50, maxHeight: "80%", anchor: "center" },

package/dist/resources/extensions/gsd/repo-identity.js

@@ -11,6 +11,7 @@ import { cpSync, existsSync, lstatSync, mkdirSync, readdirSync, readFileSync, re
 import { basename, dirname, join, resolve } from "node:path";
 import { gsdHome } from "./gsd-home.js";
 import { isGsdWorktreePath, resolveExternalStateProjectGsdFromWorktreePath, resolveExternalStateProjectIdentityFromWorktreePath, } from "./worktree-root.js";
+import { logWarning } from "./workflow-logger.js";
 function isRepoMeta(value) {
     if (!value || typeof value !== "object")
         return false;
@@ -167,7 +168,9 @@ function isProjectGsd(gsdPath) {
 }
 // ─── Repo Identity ──────────────────────────────────────────────────────────
 /**
- * Get the git remote URL for "origin", or "" if no remote is configured.
+ * Get the git remote URL for "origin", or:
+ * - "" when git cleanly reports no remote
+ * - null when git command failed (transient/unknown)
  * Uses `git config` rather than `git remote get-url` for broader compat.
  */
 function getRemoteUrl(basePath) {
@@ -179,8 +182,25 @@ function getRemoteUrl(basePath) {
             timeout: 5_000,
         }).trim();
     }
-    catch {
-        return "";
+    catch (error) {
+        const status = typeof error === "object" && error !== null && "status" in error
+            ? error.status
+            : undefined;
+        if (status === 1) {
+            try {
+                if (existsSync(join(resolveGitCommonDir(basePath), "config")))
+                    return "";
+            }
+            catch {
+                // Fall through to report unknown git/config failures.
+            }
+        }
+        // Keep transient git failures distinct from "no remote configured".
+        logWarning("state", "repo-identity: failed to resolve remote.origin.url", {
+            basePath,
+            error: String(error),
+        });
+        return null;
     }
 }
 /**
@@ -275,6 +295,16 @@ export function repoIdentity(basePath) {
         // This makes moves transparent for repos with remotes (#2750).
         return createHash("sha256").update(remoteUrl).digest("hex").slice(0, 12);
     }
+    if (remoteUrl === null) {
+        // Unknown remote status (transient git failure): prefer persisted identity.
+        const markerRoot = resolveGitRoot(basePath);
+        const markerId = readGsdIdMarker(markerRoot);
+        if (markerId) {
+            const markerPath = join(process.env.GSD_STATE_DIR || gsdHome(), "projects", markerId);
+            if (hasProjectState(markerPath) || readRepoMeta(markerPath))
+                return markerId;
+        }
+    }
     // Local-only repo: include git root since there's no remote to anchor identity.
     const root = resolveGitRoot(basePath);
     const input = `\n${root}`;
@@ -288,8 +318,7 @@ export function repoIdentity(basePath) {
  * otherwise `~/.gsd/projects/<hash>`.
  */
 export function externalGsdRoot(basePath) {
-    const base = process.env.GSD_STATE_DIR || gsdHome();
-    return join(base, "projects", repoIdentity(basePath));
+    return resolveExternalPathWithRecovery(basePath).path;
 }
 /**
  * Resolve the root directory that stores project-scoped external state.
@@ -467,6 +496,7 @@ function resolveExternalPathWithRecovery(projectPath) {
                     rmSync(markerPath, { recursive: true, force: true });
                 }
                 catch { /* non-fatal */ }
+                writeGsdIdMarker(projectPath, computedId);
             }
             catch {
                 // If migration fails, just point at the old directory.
@@ -565,7 +595,7 @@ function ensureGsdSymlinkCore(projectPath) {
     // Write repo metadata once so cleanup commands can identify this directory later.
     // Skip refresh for external-state worktrees — parent store already has metadata.
     if (!(isGsdWorktreePath(projectPath) && resolveExternalStateProjectGsdFromWorktreePath(projectPath))) {
-        writeRepoMeta(externalPath, getRemoteUrl(projectPath), resolveGitRoot(projectPath));
+        writeRepoMeta(externalPath, getRemoteUrl(projectPath) ?? "", resolveGitRoot(projectPath));
     }
     const replaceWithSymlink = () => {
         rmSync(localGsd, { recursive: true, force: true });

package/dist/resources/extensions/gsd/repository-registry.js

@@ -50,7 +50,9 @@ function resolveGitWorkingTreeRoot(basePath) {
  */
 export function createRepositoryRegistry(basePath, workspacePrefs) {
     const contract = resolveGsdPathContract(basePath);
-    const projectRoot = resolveGitWorkingTreeRoot(contract.workRoot) ?? contract.projectRoot;
+    const projectRoot = contract.isWorktree
+        ? resolveGitWorkingTreeRoot(contract.workRoot) ?? contract.projectRoot
+        : contract.projectRoot;
     const mode = workspacePrefs?.mode ?? "project";
     const repoMap = new Map();
     // "project" is reserved: always maps to projectRoot and cannot be overridden.

package/dist/resources/extensions/gsd/safety/evidence-collector.js

@@ -15,15 +15,15 @@ import { existsSync, mkdirSync, readFileSync, writeFileSync, renameSync, unlinkS
 import { join, dirname } from "node:path";
 import { randomBytes } from "node:crypto";
 const EXECUTION_TOOL_NAMES = new Set([
-    "bash",
-    "Bash",
-    "PowerShell",
     "async_bash",
+    "bash",
+    "exec_command",
+    "functions.exec_command",
     "gsd_exec",
     "gsd_exec_search",
-    "mcp__gsd-workflow__gsd_exec",
-    "mcp__gsd-workflow__gsd_exec_search",
+    "powershell",
 ]);
+const MCP_EXECUTION_TOOL_RE = /^mcp__.+__gsd_exec(?:_search)?$/;
 // ─── Module State ───────────────────────────────────────────────────────────
 let unitEvidence = [];
 // ─── Public API ─────────────────────────────────────────────────────────────
@@ -45,6 +45,13 @@ export function getFilePaths() {
         .filter((e) => e.kind === "write" || e.kind === "edit")
         .map(e => e.path);
 }
+/** True when a tool name represents a shell/command execution surface. */
+export function isExecutionToolName(name) {
+    if (typeof name !== "string")
+        return false;
+    const normalized = name.trim().toLowerCase();
+    return EXECUTION_TOOL_NAMES.has(normalized) || MCP_EXECUTION_TOOL_RE.test(normalized);
+}
 // ─── Persistence (Bug #4385 — evidence must survive session restarts) ────────
 /**
  * Build the path for the evidence JSON file for a given unit.
@@ -139,7 +146,7 @@ export function clearEvidenceFromDisk(basePath, milestoneId, sliceId, taskId) {
  * Exit codes and output are filled in by recordToolResult after execution.
  */
 export function recordToolCall(toolCallId, toolName, input) {
-    if (EXECUTION_TOOL_NAMES.has(toolName)) {
+    if (isExecutionToolName(toolName)) {
         unitEvidence.push({
             kind: "bash",
             toolCallId,