gsd-pi 2.33.1 → 2.34.0-dev.bbb5216

package/src/resources/extensions/gsd/captures.ts

@@ -9,10 +9,9 @@
  */
 
 import { existsSync, readFileSync, writeFileSync, mkdirSync } from "node:fs";
-import { join, resolve } from "node:path";
+import { join, resolve, sep } from "node:path";
 import { randomUUID } from "node:crypto";
 import { gsdRoot } from "./paths.js";
-import { resolveProjectRoot } from "./worktree.js";
 
 // ─── Types ────────────────────────────────────────────────────────────────────
 
@@ -59,8 +58,15 @@ const VALID_CLASSIFICATIONS: readonly string[] = [
  * directory that contains `.gsd/worktrees/` — that's the project root.
  */
 export function resolveCapturesPath(basePath: string): string {
-  const projectRoot = resolveProjectRoot(resolve(basePath));
-  return join(gsdRoot(projectRoot), CAPTURES_FILENAME);
+  const resolved = resolve(basePath);
+  const worktreeMarker = `${sep}.gsd${sep}worktrees${sep}`;
+  const idx = resolved.indexOf(worktreeMarker);
+  if (idx !== -1) {
+    // basePath is inside a worktree — resolve to project root
+    const projectRoot = resolved.slice(0, idx);
+    return join(projectRoot, ".gsd", CAPTURES_FILENAME);
+  }
+  return join(gsdRoot(basePath), CAPTURES_FILENAME);
 }
 
 // ─── File I/O ─────────────────────────────────────────────────────────────────

package/src/resources/extensions/gsd/commands-bootstrap.ts

@@ -0,0 +1,252 @@
+import { importExtensionModule, type ExtensionAPI, type ExtensionCommandContext } from "@gsd/pi-coding-agent";
+
+const TOP_LEVEL_SUBCOMMANDS = [
+  { cmd: "help", desc: "Categorized command reference with descriptions" },
+  { cmd: "next", desc: "Explicit step mode (same as /gsd)" },
+  { cmd: "auto", desc: "Autonomous mode — research, plan, execute, commit, repeat" },
+  { cmd: "stop", desc: "Stop auto mode gracefully" },
+  { cmd: "pause", desc: "Pause auto-mode (preserves state, /gsd auto to resume)" },
+  { cmd: "status", desc: "Progress dashboard" },
+  { cmd: "visualize", desc: "Open workflow visualizer" },
+  { cmd: "queue", desc: "Queue and reorder future milestones" },
+  { cmd: "quick", desc: "Execute a quick task without full planning overhead" },
+  { cmd: "discuss", desc: "Discuss architecture and decisions" },
+  { cmd: "capture", desc: "Fire-and-forget thought capture" },
+  { cmd: "triage", desc: "Manually trigger triage of pending captures" },
+  { cmd: "dispatch", desc: "Dispatch a specific phase directly" },
+  { cmd: "history", desc: "View execution history" },
+  { cmd: "undo", desc: "Revert last completed unit" },
+  { cmd: "skip", desc: "Prevent a unit from auto-mode dispatch" },
+  { cmd: "export", desc: "Export milestone or slice results" },
+  { cmd: "cleanup", desc: "Remove merged branches or snapshots" },
+  { cmd: "mode", desc: "Switch workflow mode (solo/team)" },
+  { cmd: "prefs", desc: "Manage preferences" },
+  { cmd: "config", desc: "Set API keys for external tools" },
+  { cmd: "keys", desc: "API key manager" },
+  { cmd: "hooks", desc: "Show configured hooks" },
+  { cmd: "run-hook", desc: "Manually trigger a specific hook" },
+  { cmd: "skill-health", desc: "Skill lifecycle dashboard" },
+  { cmd: "doctor", desc: "Runtime health checks with auto-fix" },
+  { cmd: "logs", desc: "Browse activity logs, debug logs, and metrics" },
+  { cmd: "forensics", desc: "Examine execution logs" },
+  { cmd: "init", desc: "Project init wizard" },
+  { cmd: "setup", desc: "Global setup status and configuration" },
+  { cmd: "migrate", desc: "Migrate a v1 .planning directory to .gsd format" },
+  { cmd: "remote", desc: "Control remote auto-mode" },
+  { cmd: "steer", desc: "Hard-steer plan documents during execution" },
+  { cmd: "inspect", desc: "Show SQLite DB diagnostics" },
+  { cmd: "knowledge", desc: "Add persistent project knowledge" },
+  { cmd: "new-milestone", desc: "Create a milestone from a specification document" },
+  { cmd: "parallel", desc: "Parallel milestone orchestration" },
+  { cmd: "park", desc: "Park a milestone" },
+  { cmd: "unpark", desc: "Reactivate a parked milestone" },
+  { cmd: "update", desc: "Update GSD to the latest version" },
+  { cmd: "start", desc: "Start a workflow template" },
+  { cmd: "templates", desc: "List available workflow templates" },
+  { cmd: "extensions", desc: "Manage extensions" },
+] as const;
+
+function filterStartsWith(
+  partial: string,
+  options: ReadonlyArray<{ cmd: string; desc: string }>,
+  prefix = "",
+) {
+  const normalizedPrefix = prefix.length > 0 ? `${prefix} ` : "";
+  return options
+    .filter((option) => option.cmd.startsWith(partial))
+    .map((option) => ({
+      value: `${normalizedPrefix}${option.cmd}`,
+      label: option.cmd,
+      description: option.desc,
+    }));
+}
+
+function getGsdArgumentCompletions(prefix: string) {
+  const parts = prefix.trim().split(/\s+/);
+
+  if (parts.length <= 1) {
+    return filterStartsWith(parts[0] ?? "", TOP_LEVEL_SUBCOMMANDS);
+  }
+
+  const partial = parts[1] ?? "";
+
+  if (parts[0] === "auto" && parts.length <= 2) {
+    return filterStartsWith(partial, [
+      { cmd: "--verbose", desc: "Show detailed execution output" },
+      { cmd: "--debug", desc: "Enable debug logging" },
+    ], "auto");
+  }
+
+  if (parts[0] === "next" && parts.length <= 2) {
+    return filterStartsWith(partial, [
+      { cmd: "--verbose", desc: "Show detailed step output" },
+      { cmd: "--dry-run", desc: "Preview next step without executing" },
+    ], "next");
+  }
+
+  if (parts[0] === "mode" && parts.length <= 2) {
+    return filterStartsWith(partial, [
+      { cmd: "global", desc: "Edit global workflow mode" },
+      { cmd: "project", desc: "Edit project-specific workflow mode" },
+    ], "mode");
+  }
+
+  if (parts[0] === "parallel" && parts.length <= 2) {
+    return filterStartsWith(partial, [
+      { cmd: "start", desc: "Start parallel milestone orchestration" },
+      { cmd: "status", desc: "Show parallel worker statuses" },
+      { cmd: "stop", desc: "Stop all parallel workers" },
+      { cmd: "pause", desc: "Pause a specific worker" },
+      { cmd: "resume", desc: "Resume a paused worker" },
+      { cmd: "merge", desc: "Merge completed milestone branches" },
+    ], "parallel");
+  }
+
+  if (parts[0] === "setup" && parts.length <= 2) {
+    return filterStartsWith(partial, [
+      { cmd: "llm", desc: "Configure LLM provider settings" },
+      { cmd: "search", desc: "Configure web search provider" },
+      { cmd: "remote", desc: "Configure remote integrations" },
+      { cmd: "keys", desc: "Manage API keys" },
+      { cmd: "prefs", desc: "Configure global preferences" },
+    ], "setup");
+  }
+
+  if (parts[0] === "logs" && parts.length <= 2) {
+    return filterStartsWith(partial, [
+      { cmd: "debug", desc: "List or view debug log files" },
+      { cmd: "tail", desc: "Show last N activity log summaries" },
+      { cmd: "clear", desc: "Remove old activity and debug logs" },
+    ], "logs");
+  }
+
+  if (parts[0] === "keys" && parts.length <= 2) {
+    return filterStartsWith(partial, [
+      { cmd: "list", desc: "Show key status dashboard" },
+      { cmd: "add", desc: "Add a key for a provider" },
+      { cmd: "remove", desc: "Remove a key" },
+      { cmd: "test", desc: "Validate key(s) with API call" },
+      { cmd: "rotate", desc: "Replace an existing key" },
+      { cmd: "doctor", desc: "Health check all keys" },
+    ], "keys");
+  }
+
+  if (parts[0] === "prefs" && parts.length <= 2) {
+    return filterStartsWith(partial, [
+      { cmd: "global", desc: "Edit global preferences file" },
+      { cmd: "project", desc: "Edit project preferences file" },
+      { cmd: "status", desc: "Show effective preferences" },
+      { cmd: "wizard", desc: "Interactive preferences wizard" },
+      { cmd: "setup", desc: "First-time preferences setup" },
+      { cmd: "import-claude", desc: "Import settings from Claude Code" },
+    ], "prefs");
+  }
+
+  if (parts[0] === "remote" && parts.length <= 2) {
+    return filterStartsWith(partial, [
+      { cmd: "slack", desc: "Configure Slack integration" },
+      { cmd: "discord", desc: "Configure Discord integration" },
+      { cmd: "status", desc: "Show remote connection status" },
+      { cmd: "disconnect", desc: "Disconnect remote integrations" },
+    ], "remote");
+  }
+
+  if (parts[0] === "history" && parts.length <= 2) {
+    return filterStartsWith(partial, [
+      { cmd: "--cost", desc: "Show cost breakdown per entry" },
+      { cmd: "--phase", desc: "Filter by phase type" },
+      { cmd: "--model", desc: "Filter by model used" },
+      { cmd: "10", desc: "Show last 10 entries" },
+      { cmd: "20", desc: "Show last 20 entries" },
+      { cmd: "50", desc: "Show last 50 entries" },
+    ], "history");
+  }
+
+  if (parts[0] === "export" && parts.length <= 2) {
+    return filterStartsWith(partial, [
+      { cmd: "--json", desc: "Export as JSON" },
+      { cmd: "--markdown", desc: "Export as Markdown" },
+      { cmd: "--html", desc: "Export as HTML" },
+      { cmd: "--html --all", desc: "Export all milestones as HTML" },
+    ], "export");
+  }
+
+  if (parts[0] === "cleanup" && parts.length <= 2) {
+    return filterStartsWith(partial, [
+      { cmd: "branches", desc: "Remove merged milestone branches" },
+      { cmd: "snapshots", desc: "Remove old execution snapshots" },
+    ], "cleanup");
+  }
+
+  if (parts[0] === "knowledge" && parts.length <= 2) {
+    return filterStartsWith(partial, [
+      { cmd: "rule", desc: "Add a project rule" },
+      { cmd: "pattern", desc: "Add a code pattern" },
+      { cmd: "lesson", desc: "Record a lesson learned" },
+    ], "knowledge");
+  }
+
+  if (parts[0] === "start" && parts.length <= 2) {
+    return filterStartsWith(partial, [
+      { cmd: "bugfix", desc: "Triage, fix, test, and ship a bug fix" },
+      { cmd: "small-feature", desc: "Lightweight feature with optional discussion" },
+      { cmd: "spike", desc: "Research, prototype, and document findings" },
+      { cmd: "hotfix", desc: "Minimal: fix it, test it, ship it" },
+      { cmd: "refactor", desc: "Inventory, plan waves, migrate, verify" },
+      { cmd: "security-audit", desc: "Scan, triage, remediate, re-scan" },
+      { cmd: "dep-upgrade", desc: "Assess, upgrade, fix breaks, verify" },
+      { cmd: "full-project", desc: "Complete GSD workflow with full ceremony" },
+      { cmd: "resume", desc: "Resume an in-progress workflow" },
+      { cmd: "--list", desc: "List all available templates" },
+      { cmd: "--dry-run", desc: "Preview workflow without executing" },
+    ], "start");
+  }
+
+  if (parts[0] === "templates" && parts.length <= 2) {
+    return filterStartsWith(partial, [
+      { cmd: "info", desc: "Show detailed template info" },
+    ], "templates");
+  }
+
+  if (parts[0] === "extensions" && parts.length <= 2) {
+    return filterStartsWith(partial, [
+      { cmd: "list", desc: "List all extensions and their status" },
+      { cmd: "enable", desc: "Enable a disabled extension" },
+      { cmd: "disable", desc: "Disable an extension" },
+      { cmd: "info", desc: "Show extension details" },
+    ], "extensions");
+  }
+
+  if (parts[0] === "doctor" && parts.length <= 2) {
+    return filterStartsWith(partial, [
+      { cmd: "fix", desc: "Auto-fix detected issues" },
+      { cmd: "heal", desc: "AI-driven deep healing" },
+      { cmd: "audit", desc: "Run health audit without fixing" },
+    ], "doctor");
+  }
+
+  if (parts[0] === "dispatch" && parts.length <= 2) {
+    return filterStartsWith(partial, [
+      { cmd: "research", desc: "Run research phase" },
+      { cmd: "plan", desc: "Run planning phase" },
+      { cmd: "execute", desc: "Run execution phase" },
+      { cmd: "complete", desc: "Run completion phase" },
+      { cmd: "reassess", desc: "Reassess current progress" },
+      { cmd: "uat", desc: "Run user acceptance testing" },
+      { cmd: "replan", desc: "Replan the current slice" },
+    ], "dispatch");
+  }
+
+  return null;
+}
+
+export function registerLazyGSDCommand(pi: ExtensionAPI): void {
+  pi.registerCommand("gsd", {
+    description: "GSD — Get Shit Done",
+    getArgumentCompletions: getGsdArgumentCompletions,
+    handler: async (args: string, ctx: ExtensionCommandContext) => {
+      const { handleGSDCommand } = await importExtensionModule<typeof import("./commands.js")>(import.meta.url, "./commands.js");
+      await handleGSDCommand(args, ctx, pi);
+    },
+  });
+}

package/src/resources/extensions/gsd/commands.ts

@@ -416,36 +416,46 @@ export function registerGSDCommand(pi: ExtensionAPI): void {
     },
 
     async handler(args: string, ctx: ExtensionCommandContext) {
-      const trimmed = (typeof args === "string" ? args : "").trim();
+      await handleGSDCommand(args, ctx, pi);
+    },
+  });
+}
 
-      if (trimmed === "help" || trimmed === "h" || trimmed === "?") {
-        showHelp(ctx);
-        return;
-      }
+export async function handleGSDCommand(
+  args: string,
+  ctx: ExtensionCommandContext,
+  pi: ExtensionAPI,
+): Promise<void> {
+  const trimmed = (typeof args === "string" ? args : "").trim();
 
-      if (trimmed === "status") {
-        await handleStatus(ctx);
-        return;
-      }
+  if (trimmed === "help" || trimmed === "h" || trimmed === "?") {
+    showHelp(ctx);
+    return;
+  }
 
-      if (trimmed === "visualize") {
-        await handleVisualize(ctx);
-        return;
-      }
+  if (trimmed === "status") {
+    await handleStatus(ctx);
+    return;
+  }
 
-      if (trimmed === "mode" || trimmed.startsWith("mode ")) {
-        const modeArgs = trimmed.replace(/^mode\s*/, "").trim();
-        const scope = modeArgs === "project" ? "project" : "global";
-        const path = scope === "project" ? getProjectGSDPreferencesPath() : getGlobalGSDPreferencesPath();
-        await ensurePreferencesFile(path, ctx, scope);
-        await handlePrefsMode(ctx, scope);
-        return;
-      }
+  if (trimmed === "visualize") {
+    await handleVisualize(ctx);
+    return;
+  }
 
-      if (trimmed === "prefs" || trimmed.startsWith("prefs ")) {
-        await handlePrefs(trimmed.replace(/^prefs\s*/, "").trim(), ctx);
-        return;
-      }
+  if (trimmed === "mode" || trimmed.startsWith("mode ")) {
+    const modeArgs = trimmed.replace(/^mode\s*/, "").trim();
+    const scope = modeArgs === "project" ? "project" : "global";
+    const path = scope === "project" ? getProjectGSDPreferencesPath() : getGlobalGSDPreferencesPath();
+    await ensurePreferencesFile(path, ctx, scope);
+    await handlePrefsMode(ctx, scope);
+    return;
+  }
+
+  if (trimmed === "prefs" || trimmed.startsWith("prefs ")) {
+    await handlePrefs(trimmed.replace(/^prefs\s*/, "").trim(), ctx);
+    return;
+  }
 
       if (trimmed === "init") {
         const { detectProjectState } = await import("./detection.js");
@@ -893,12 +903,10 @@ Examples:
         return;
       }
 
-      ctx.ui.notify(
-        `Unknown: /gsd ${trimmed}. Run /gsd help for available commands.`,
-        "warning",
-      );
-    },
-  });
+  ctx.ui.notify(
+    `Unknown: /gsd ${trimmed}. Run /gsd help for available commands.`,
+    "warning",
+  );
 }
 
 function showHelp(ctx: ExtensionCommandContext): void {

package/src/resources/extensions/gsd/dispatch-guard.ts

@@ -5,7 +5,6 @@ import { readdirSync } from "node:fs";
 import { resolveMilestoneFile, milestonesDir } from "./paths.js";
 import { parseRoadmapSlices } from "./roadmap-slices.js";
 import { findMilestoneIds } from "./guided-flow.js";
-import { parseUnitId } from "./unit-id.js";
 
 const SLICE_DISPATCH_TYPES = new Set([
   "research-slice",
@@ -37,10 +36,15 @@ function readRoadmapFromDisk(base: string, milestoneId: string): string | null {
   }
 }
 
-export function getPriorSliceCompletionBlocker(base: string, _mainBranch: string, unitType: string, unitId: string): string | null {
+export function getPriorSliceCompletionBlocker(
+  base: string,
+  _mainBranch: string,
+  unitType: string,
+  unitId: string,
+): string | null {
   if (!SLICE_DISPATCH_TYPES.has(unitType)) return null;
 
-  const { milestone: targetMid, slice: targetSid } = parseUnitId(unitId);
+  const [targetMid, targetSid] = unitId.split("/");
   if (!targetMid || !targetSid) return null;
 
   // Use findMilestoneIds to respect custom queue order.
@@ -51,9 +55,7 @@ export function getPriorSliceCompletionBlocker(base: string, _mainBranch: string
   const milestoneIds = allIds.slice(0, targetIdx + 1);
 
   for (const mid of milestoneIds) {
-    // Skip parked milestones — they don't block dispatch of later milestones
-    const parkedFile = resolveMilestoneFile(base, mid, "PARKED");
-    if (parkedFile) continue;
+    if (resolveMilestoneFile(base, mid, "PARKED")) continue;
 
     // Read from disk (working tree) — always has the latest state
     const roadmapContent = readRoadmapFromDisk(base, mid);
@@ -61,17 +63,19 @@ export function getPriorSliceCompletionBlocker(base: string, _mainBranch: string
 
     const slices = parseRoadmapSlices(roadmapContent);
     if (mid !== targetMid) {
-      const incomplete = slices.find(slice => !slice.done);
+      const incomplete = slices.find((slice) => !slice.done);
       if (incomplete) {
         return `Cannot dispatch ${unitType} ${unitId}: earlier slice ${mid}/${incomplete.id} is not complete.`;
       }
       continue;
     }
 
-    const targetIndex = slices.findIndex(slice => slice.id === targetSid);
+    const targetIndex = slices.findIndex((slice) => slice.id === targetSid);
     if (targetIndex === -1) return null;
 
-    const incomplete = slices.slice(0, targetIndex).find(slice => !slice.done);
+    const incomplete = slices
+      .slice(0, targetIndex)
+      .find((slice) => !slice.done);
     if (incomplete) {
       return `Cannot dispatch ${unitType} ${unitId}: earlier slice ${targetMid}/${incomplete.id} is not complete.`;
     }

package/src/resources/extensions/gsd/docs/preferences-reference.md

@@ -21,7 +21,12 @@ Full documentation for `~/.gsd/preferences.md` (global) and `.gsd/preferences.md
 **Empty arrays (`[]`) are equivalent to omitting the field entirely.** During validation, GSD deletes empty arrays from the preferences object (see `validatePreferences()` in `preferences.ts`):
 
 ```typescript
-for (const key of ["always_use_skills", "prefer_skills", "avoid_skills", "custom_instructions"] as const) {
+for (const key of [
+  "always_use_skills",
+  "prefer_skills",
+  "avoid_skills",
+  "custom_instructions",
+] as const) {
   if (validated[key] && validated[key]!.length === 0) {
     delete validated[key];
   }
@@ -50,6 +55,7 @@ Preferences are loaded from two locations and merged:
 2. **Project:** `.gsd/preferences.md` — applies to the current project only
 
 **Merge behavior** (see `mergePreferences()` in `preferences.ts`):
+
 - **Scalar fields** (`skill_discovery`, `budget_ceiling`, etc.): Project wins if defined, otherwise global. Uses nullish coalescing (`??`).
 - **Array fields** (`always_use_skills`, `prefer_skills`, etc.): Concatenated via `mergeStringLists()` (global first, then project).
 - **Object fields** (`models`, `git`, `auto_supervisor`): Shallow merge via spread operator `{ ...base, ...override }`.
@@ -60,10 +66,10 @@ For `models`, project settings override global at the phase level. If global has
 
 These are **separate concerns**:
 
-| Field | What it controls | Code reference |
-|-------|-----------------|----------------|
-| `skill_discovery` | **Whether** GSD looks for relevant skills during research | `resolveSkillDiscoveryMode()` in `preferences.ts` |
-| `always_use_skills`, `prefer_skills`, `avoid_skills` | **Which** skills to use when they're found relevant | `renderPreferencesForSystemPrompt()` in `preferences.ts` |
+| Field                                                | What it controls                                          | Code reference                                           |
+| ---------------------------------------------------- | --------------------------------------------------------- | -------------------------------------------------------- |
+| `skill_discovery`                                    | **Whether** GSD looks for relevant skills during research | `resolveSkillDiscoveryMode()` in `preferences.ts`        |
+| `always_use_skills`, `prefer_skills`, `avoid_skills` | **Which** skills to use when they're found relevant       | `renderPreferencesForSystemPrompt()` in `preferences.ts` |
 
 Setting `prefer_skills: []` does **not** disable skill discovery — it just means you have no preference overrides. Use `skill_discovery: off` to disable discovery entirely.
 
@@ -75,14 +81,14 @@ Setting `prefer_skills: []` does **not** disable skill discovery — it just mea
 
 - `mode`: workflow mode — `"solo"` or `"team"`. Sets sensible defaults for git and project settings based on your workflow. Mode defaults are the lowest priority layer — any explicit preference overrides them. Omit to configure everything manually.
 
-  | Setting | `solo` | `team` |
-  |---|---|---|
-  | `git.auto_push` | `true` | `false` |
-  | `git.push_branches` | `false` | `true` |
-  | `git.pre_merge_check` | `false` | `true` |
-  | `git.merge_strategy` | `"squash"` | `"squash"` |
-  | `git.isolation` | `"worktree"` | `"worktree"` |
-  | `unique_milestone_ids` | `false` | `true` |
+  | Setting                | `solo`       | `team`       |
+  | ---------------------- | ------------ | ------------ |
+  | `git.auto_push`        | `true`       | `false`      |
+  | `git.push_branches`    | `false`      | `true`       |
+  | `git.pre_merge_check`  | `false`      | `true`       |
+  | `git.merge_strategy`   | `"squash"`   | `"squash"`   |
+  | `git.isolation`        | `"worktree"` | `"worktree"` |
+  | `unique_milestone_ids` | `false`      | `true`       |
 
   Quick setup: `/gsd mode` (global) or `/gsd mode project` (project-level).
 
@@ -141,11 +147,12 @@ Setting `prefer_skills: []` does **not** disable skill discovery — it just mea
 
 - `context_pause_threshold`: number (0-100) — context window usage percentage at which auto-mode should pause to suggest checkpointing. Set to `0` to disable. Default: `0` (disabled).
 
-- `token_profile`: `"budget"`, `"balanced"`, or `"quality"` — coordinates model selection, phase skipping, and context compression. `budget` skips research/reassessment and uses cheaper models; `balanced` (default) runs all phases; `quality` prefers higher-quality models. See token-optimization docs.
+- `token_profile`: `"budget"`, `"balanced"`, or `"quality"` — coordinates model selection, phase skipping, and context compression. `budget` skips research/reassessment and uses cheaper models; `balanced` (default) skips research/reassessment to reduce token burn; `quality` prefers higher-quality models. See token-optimization docs.
 
 - `phases`: fine-grained control over which phases run. Usually set by `token_profile`, but can be overridden. Keys:
   - `skip_research`: boolean — skip milestone-level research. Default: `false`.
-  - `skip_reassess`: boolean — skip roadmap reassessment after each slice. Default: `false`.
+  - `reassess_after_slice`: boolean — run roadmap reassessment after each completed slice. Default: `false`.
+  - `skip_reassess`: boolean — force-disable roadmap reassessment even if `reassess_after_slice` is enabled. Default: `false`.
   - `skip_slice_research`: boolean — skip per-slice research. Default: `false`.
 
 - `remote_questions`: route interactive questions to Slack/Discord for headless auto-mode. Keys:
@@ -359,11 +366,11 @@ If you use a bare model ID (no provider prefix) and it exists in multiple provid
 ---
 version: 1
 models:
-  research: openrouter/deepseek/deepseek-r1  # $0.28/$0.42 per 1M tokens
+  research: openrouter/deepseek/deepseek-r1 # $0.28/$0.42 per 1M tokens
   planning:
-    model: claude-opus-4-6                   # $5/$25 — best for architecture
+    model: claude-opus-4-6 # $5/$25 — best for architecture
     fallbacks:
-      - openrouter/z-ai/glm-5                # $1/$3.20 — strong alternative
+      - openrouter/z-ai/glm-5 # $1/$3.20 — strong alternative
   execution: openrouter/minimax/minimax-m2.5 # $0.30/$1.20 — cheapest quality
   completion: openrouter/minimax/minimax-m2.5
 ---

package/src/resources/extensions/gsd/doctor-checks.ts

@@ -314,10 +314,9 @@ export async function checkRuntimeHealth(
         });
 
         if (shouldFix("orphaned_completed_units")) {
-          const { removePersistedKey } = await import("./auto-recovery.js");
-          for (const key of orphaned) {
-            removePersistedKey(basePath, key);
-          }
+          const orphanedSet = new Set(orphaned);
+          const remaining = keys.filter((key) => !orphanedSet.has(key));
+          await saveFile(completedKeysFile, JSON.stringify(remaining));
           fixesApplied.push(`removed ${orphaned.length} orphaned completed-unit key(s)`);
         }
       }

package/src/resources/extensions/gsd/git-service.ts

@@ -42,6 +42,8 @@ export interface GitPreferences {
   push_branches?: boolean;
   remote?: string;
   snapshots?: boolean;
+  /** Deprecated. .gsd/ is managed externally; retained for compatibility. */
+  commit_docs?: boolean;
   pre_merge_check?: boolean | string;
   commit_type?: string;
   main_branch?: string;
@@ -223,9 +225,21 @@ export function readIntegrationBranch(basePath: string, milestoneId: string): st
  *
  * The file is committed immediately so the metadata is persisted in git.
  */
-export function writeIntegrationBranch(basePath: string, milestoneId: string, branch: string): void {
+/** Regex matching GSD quick-task branches: gsd/quick/<num>-<slug> */
+export const QUICK_BRANCH_RE = /^gsd\/quick\//;
+
+export function writeIntegrationBranch(
+  basePath: string,
+  milestoneId: string,
+  branch: string,
+  _options?: { commitDocs?: boolean },
+): void {
   // Don't record slice branches as the integration target
   if (SLICE_BRANCH_RE.test(branch)) return;
+  // Don't record quick-task branches — they are ephemeral and merge back
+  // to their origin branch on completion. Recording one as the integration
+  // target causes milestone merges to land on the wrong branch (#1293).
+  if (QUICK_BRANCH_RE.test(branch)) return;
   // Validate
   if (!VALID_BRANCH_NAME.test(branch)) return;
   // Skip if already recorded with the same branch (idempotent across restarts).
@@ -336,13 +350,17 @@ export class GitServiceImpl {
    * @param extraExclusions Additional pathspec exclusions beyond RUNTIME_EXCLUSION_PATHS.
    */
   private smartStage(extraExclusions: readonly string[] = []): void {
-    // Always exclude .gsd/ — state is managed externally (symlinked to ~/.gsd/projects/<hash>/)
-    const allExclusions = [".gsd/", ...extraExclusions];
-
     // One-time cleanup: if runtime files are already tracked in the index
     // (from older versions where the fallback bug staged them), untrack them
     // in a dedicated commit. This must happen as a separate commit because
     // the git reset HEAD step below would otherwise undo the rm --cached.
+    //
+    // SAFETY: Only untrack the specific RUNTIME paths (activity/, runtime/,
+    // auto.lock, etc.) — NOT all of .gsd/. If .gsd/milestones/ files were
+    // previously tracked, they stay tracked until the milestone completes
+    // and the worktree is torn down. This prevents a mid-execution behavioral
+    // discontinuity where the first half of a milestone has .gsd/ artifacts
+    // committed but the second half doesn't (#1326).
     if (!this._runtimeFilesCleanedUp) {
       let cleaned = false;
       for (const exclusion of RUNTIME_EXCLUSION_PATHS) {
@@ -357,17 +375,19 @@ export class GitServiceImpl {
 
     // Stage everything, then unstage excluded paths.
     //
-    // Previous approach used pathspec excludes (:(exclude)...) with git add -A,
-    // but that fails when .gsd/ is in .gitignore — git exits non-zero before
-    // evaluating the excludes. The catch fallback ran plain `git add -A`,
-    // staging all tracked runtime files unconditionally and defeating the
-    // exclusion list entirely.
+    // Exclude only RUNTIME paths from staging — not the entire .gsd/ directory.
+    // When .gsd/milestones/ files are already tracked in the index (projects
+    // where .gsd/ is not gitignored, or Windows junctions that git sees as
+    // real directories), they should continue to be committed. Excluding the
+    // entire .gsd/ directory mid-milestone causes silent commit failure where
+    // the second half of a milestone's artifacts are never committed (#1326).
     //
-    // git reset HEAD silently succeeds when the path isn't staged, so no
-    // error handling is needed per-path.
+    // If .gsd/ IS in .gitignore (the default for external state projects),
+    // git add -A already skips it and the reset is a harmless no-op.
     nativeAddAll(this.basePath);
 
-    for (const exclusion of allExclusions) {
+    const runtimeExclusions = [...RUNTIME_EXCLUSION_PATHS, ...extraExclusions];
+    for (const exclusion of runtimeExclusions) {
       try { nativeResetPaths(this.basePath, [exclusion]); } catch { /* path not staged — ignore */ }
     }
   }

package/src/resources/extensions/gsd/gitignore.ts

@@ -86,7 +86,10 @@ const BASELINE_PATTERNS = [
  * `.gsd/` state is managed externally (symlinked to `~/.gsd/projects/<hash>/`),
  * so the entire directory is always gitignored.
  */
-export function ensureGitignore(basePath: string, options?: { manageGitignore?: boolean }): boolean {
+export function ensureGitignore(
+  basePath: string,
+  options?: { manageGitignore?: boolean; commitDocs?: boolean },
+): boolean {
   // If manage_gitignore is explicitly false, do not touch .gitignore at all
   if (options?.manageGitignore === false) return false;
 
@@ -212,4 +215,3 @@ custom_instructions:
   return true;
 }
 
-