gsd-pi 2.76.0 → 2.77.0-dev.2daa994b6

package/src/resources/extensions/gsd/pre-execution-checks.ts

@@ -91,8 +91,13 @@ export function extractPackageReferences(description: string): string[] {
     }
   }
 
-  // require('pkg') or import from 'pkg' in code blocks
-  const importPattern = /(?:require\s*\(\s*['"]|from\s+['"])([a-zA-Z0-9@/_-]+)['"\)]/g;
+  // require('pkg') or `import ... from 'pkg'` in code blocks.
+  // The `from\s+['"]` branch MUST be preceded by an `import` keyword so that
+  // natural-language prose like `from "What's Next"` or `from 'master'` does
+  // not produce false package-existence failures.  Requiring the leading import
+  // keyword anchors the match to JavaScript/TypeScript syntax.
+  // See: https://github.com/gsd-build/gsd-2/issues/4388
+  const importPattern = /(?:require\s*\(\s*['"]|import\b[\s\S]*?\bfrom\s+['"])([a-zA-Z0-9@/_-]+)['"\)]/g;
   let importMatch: RegExpExecArray | null;
   while ((importMatch = importPattern.exec(description)) !== null) {
     // Skip relative imports and node builtins
@@ -323,9 +328,24 @@ function extractPathFromAnnotation(raw: string): string {
     return backtickMatch[2].trim();
   }
 
+  // Strip leading/trailing double or single quotes wrapping the whole value.
+  // Plan documents sometimes emit `"src/foo.ts"` or `'src/bar.ts'` as input
+  // annotations. Stripping the wrapper allows the inner path to be checked
+  // correctly instead of producing a false-positive "file not found" error
+  // for a literal string with quote characters in it (#3747).
+  const quoteMatch = trimmed.match(/^(["'])([^"']+)\1$/);
+  if (quoteMatch) {
+    return quoteMatch[2].trim();
+  }
+
   const annotatedMatch = trimmed.match(/^(.+?)\s+[—–-]\s+.+$/);
   if (annotatedMatch) {
-    return annotatedMatch[1].trim();
+    const prefix = annotatedMatch[1].trim();
+    const prefixBacktickMatch = prefix.match(/`([^`]+)`/);
+    if (prefixBacktickMatch && looksLikePathOrUrl(prefixBacktickMatch[1].trim())) {
+      return prefixBacktickMatch[1].trim();
+    }
+    return prefix.replace(/`/g, "").trim();
   }
 
   // Fallback: scan all backticked tokens and return the first one that looks
@@ -388,13 +408,19 @@ function containsGlobPattern(candidate: string): boolean {
 
 /**
  * Build a set of files that will be created by tasks up to (but not including) taskIndex.
+ * Also includes outputs of completed tasks at any position — a completed task has already
+ * run and its outputs are available regardless of sequence position or disk state (#4071).
  * All paths are normalized for consistent comparison.
  */
 function getExpectedOutputsUpTo(tasks: TaskRow[], taskIndex: number): Set<string> {
   const outputs = new Set<string>();
-  for (let i = 0; i < taskIndex; i++) {
-    for (const file of tasks[i].expected_output) {
-      outputs.add(normalizeFilePath(file));
+  for (let i = 0; i < tasks.length; i++) {
+    const task = tasks[i];
+    // Include prior tasks (i < taskIndex) OR completed tasks at any position
+    if (i < taskIndex || task.status === "completed") {
+      for (const file of task.expected_output) {
+        outputs.add(normalizeFilePath(file));
+      }
     }
   }
   return outputs;
@@ -481,13 +507,19 @@ export function checkTaskOrdering(
   const results: PreExecutionCheckJSON[] = [];
 
   // Build map: normalized file → task index that creates it
-  const fileCreators = new Map<string, { taskId: string; index: number; originalPath: string }>();
+  const fileCreators = new Map<string, { taskId: string; index: number; originalPath: string; completed: boolean }>();
   for (let i = 0; i < tasks.length; i++) {
     const task = tasks[i];
     for (const file of task.expected_output) {
       const normalizedFile = normalizeFilePath(file);
-      if (!fileCreators.has(normalizedFile)) {
-        fileCreators.set(normalizedFile, { taskId: task.id, index: i, originalPath: file });
+      const existing = fileCreators.get(normalizedFile);
+      if (!existing || (!existing.completed && task.status === "completed")) {
+        fileCreators.set(normalizedFile, {
+          taskId: task.id,
+          index: i,
+          originalPath: file,
+          completed: task.status === "completed",
+        });
       }
     }
   }
@@ -511,7 +543,11 @@ export function checkTaskOrdering(
       const creator = fileCreators.get(normalizedFile);
       const absolutePath = resolve(basePath, normalizedFile);
       const existsOnDisk = existsSync(absolutePath);
-      if (creator && creator.index > i && !existsOnDisk) {
+      // Skip if the creating task has already completed — its output is available
+      // regardless of disk state (e.g. file was a temp artifact cleaned up after
+      // the task ran, or a replan introduced a new earlier-sequence task that
+      // reads this pre-execution output). (#4071)
+      if (creator && creator.index > i && !existsOnDisk && !creator.completed) {
         // Task reads file that is created later — impossible ordering
         results.push({
           category: "file",

package/src/resources/extensions/gsd/preferences-types.ts

@@ -28,6 +28,37 @@ export interface ContextManagementConfig {
   compaction_threshold_percent?: number;  // default: 0.70, range: 0.5-0.95
   tool_result_max_chars?: number;         // default: 800, range: 200-10000
 }
+
+/**
+ * Opt-in tool-output sandboxing for sub-sessions. When enabled, the gsd_exec
+ * MCP tool runs scripts in an isolated subprocess and returns only a short
+ * digest to the calling agent's context window; full stdout/stderr persist
+ * in the project memory store and can be retrieved by id later.
+ *
+ * Inspired by mksglu/context-mode (Elastic License 2.0). This is an
+ * independent implementation — no upstream code is incorporated.
+ */
+export interface ContextModeConfig {
+  /** Master switch. Default: true (opt-out via `enabled: false`). */
+  enabled?: boolean;
+  /** Per-invocation timeout in milliseconds. Default: 30_000. Range: 1_000–600_000. */
+  exec_timeout_ms?: number;
+  /** Cap on persisted stdout bytes per invocation. Default: 1_048_576 (1 MiB). Range: 4_096–16_777_216. */
+  exec_stdout_cap_bytes?: number;
+  /** Number of trailing stdout characters returned in the digest. Default: 300. Range: 0–4_000. */
+  exec_digest_chars?: number;
+  /** Environment variables forwarded to sandboxed processes (case-sensitive names). PATH and HOME are always forwarded. */
+  exec_env_allowlist?: string[];
+}
+
+/**
+ * Resolve whether context-mode features (gsd_exec sandbox + compaction
+ * snapshot) should be active. Default is ON: missing config or missing
+ * `enabled` is treated as true. Only `enabled: false` disables.
+ */
+export function isContextModeEnabled(prefs: { context_mode?: ContextModeConfig } | null | undefined): boolean {
+  return prefs?.context_mode?.enabled !== false;
+}
 import type { GitHubSyncConfig } from "../github-sync/types.js";
 
 // ─── Workflow Modes ──────────────────────────────────────────────────────────
@@ -117,6 +148,7 @@ export const KNOWN_PREFERENCE_KEYS = new Set<string>([
   "flat_rate_providers",
   "language",
   "context_window_override",
+  "context_mode",
 ]);
 
 /** Canonical list of all dispatch unit types. */
@@ -300,6 +332,12 @@ export interface GSDPreferences {
    */
   context_window_override?: number;
   context_management?: ContextManagementConfig;
+  /**
+   * Tool-output sandboxing via gsd_exec. Keeps sub-session context windows
+   * clean by running scripts in a subprocess and only surfacing a short
+   * digest. See `ContextModeConfig`. Default: disabled.
+   */
+  context_mode?: ContextModeConfig;
   token_profile?: TokenProfile;
   phases?: PhaseSkipPreferences;
   auto_visualize?: boolean;
@@ -354,6 +392,14 @@ export interface GSDPreferences {
     checkpoints?: boolean;
     auto_rollback?: boolean;
     timeout_scale_cap?: number;
+    /**
+     * Glob patterns for files that are always expected side-effects of any task.
+     * Files matching any pattern here are excluded from unexpected-change warnings.
+     * Supports standard glob syntax (e.g. `tracking/history/**`, `*.log`).
+     * Fixes #4385/#4436 — audit-trail snapshots, build artifacts, and other
+     * project-level secondary writes shouldn't require per-task declaration.
+     */
+    file_change_allowlist?: string[];
   };
 
 

package/src/resources/extensions/gsd/preferences-validation.ts

@@ -644,6 +644,50 @@ export function validatePreferences(preferences: GSDPreferences): {
     }
   }
 
+  // ─── Context Mode (gsd_exec sandbox) ────────────────────────────────────
+  if (preferences.context_mode !== undefined) {
+    if (typeof preferences.context_mode === "object" && preferences.context_mode !== null) {
+      const cmode = preferences.context_mode as unknown as Record<string, unknown>;
+      const validCmode: Record<string, unknown> = {};
+
+      if (cmode.enabled !== undefined) {
+        if (typeof cmode.enabled === "boolean") validCmode.enabled = cmode.enabled;
+        else errors.push("context_mode.enabled must be a boolean");
+      }
+      if (cmode.exec_timeout_ms !== undefined) {
+        const t = cmode.exec_timeout_ms;
+        if (typeof t === "number" && t >= 1000 && t <= 600_000) validCmode.exec_timeout_ms = Math.floor(t);
+        else errors.push("context_mode.exec_timeout_ms must be a number between 1000 and 600000");
+      }
+      if (cmode.exec_stdout_cap_bytes !== undefined) {
+        const b = cmode.exec_stdout_cap_bytes;
+        if (typeof b === "number" && b >= 4096 && b <= 16_777_216) validCmode.exec_stdout_cap_bytes = Math.floor(b);
+        else errors.push("context_mode.exec_stdout_cap_bytes must be a number between 4096 and 16777216");
+      }
+      if (cmode.exec_digest_chars !== undefined) {
+        const c = cmode.exec_digest_chars;
+        if (typeof c === "number" && c >= 0 && c <= 4000) validCmode.exec_digest_chars = Math.floor(c);
+        else errors.push("context_mode.exec_digest_chars must be a number between 0 and 4000");
+      }
+      if (cmode.exec_env_allowlist !== undefined) {
+        if (
+          Array.isArray(cmode.exec_env_allowlist) &&
+          cmode.exec_env_allowlist.every((v) => typeof v === "string" && /^[A-Z_][A-Z0-9_]*$/i.test(v))
+        ) {
+          validCmode.exec_env_allowlist = cmode.exec_env_allowlist;
+        } else {
+          errors.push("context_mode.exec_env_allowlist must be an array of valid env var names");
+        }
+      }
+
+      if (Object.keys(validCmode).length > 0) {
+        validated.context_mode = validCmode as any;
+      }
+    } else {
+      errors.push("context_mode must be an object");
+    }
+  }
+
   // ─── Parallel Config ────────────────────────────────────────────────────
   if (preferences.parallel && typeof preferences.parallel === "object") {
     const p = preferences.parallel as unknown as Record<string, unknown>;
@@ -697,6 +741,41 @@ export function validatePreferences(preferences: GSDPreferences): {
     }
   }
 
+  // ─── Slice Parallel Config ───────────────────────────────────────────────
+  if (preferences.slice_parallel !== undefined) {
+    if (typeof preferences.slice_parallel === "object" && preferences.slice_parallel !== null) {
+      const sp = preferences.slice_parallel as Record<string, unknown>;
+      const validSp: NonNullable<GSDPreferences["slice_parallel"]> = {};
+
+      if (sp.enabled !== undefined) {
+        if (typeof sp.enabled === "boolean") validSp.enabled = sp.enabled;
+        else errors.push("slice_parallel.enabled must be a boolean");
+      }
+
+      if (sp.max_workers !== undefined) {
+        const maxWorkers = typeof sp.max_workers === "number" ? sp.max_workers : Number(sp.max_workers);
+        if (Number.isFinite(maxWorkers) && maxWorkers >= 1 && maxWorkers <= 8) {
+          validSp.max_workers = Math.floor(maxWorkers);
+        } else {
+          errors.push("slice_parallel.max_workers must be a number between 1 and 8");
+        }
+      }
+
+      const knownSliceParallelKeys = new Set(["enabled", "max_workers"]);
+      for (const key of Object.keys(sp)) {
+        if (!knownSliceParallelKeys.has(key)) {
+          warnings.push(`unknown slice_parallel key "${key}" — ignored`);
+        }
+      }
+
+      if (Object.keys(validSp).length > 0) {
+        validated.slice_parallel = validSp;
+      }
+    } else {
+      errors.push("slice_parallel must be an object");
+    }
+  }
+
   // ─── Reactive Execution ─────────────────────────────────────────────────
   if (preferences.reactive_execution !== undefined) {
     if (typeof preferences.reactive_execution === "object" && preferences.reactive_execution !== null) {
@@ -908,6 +987,27 @@ export function validatePreferences(preferences: GSDPreferences): {
     if (g.merge_to_main !== undefined) {
       warnings.push("git.merge_to_main is deprecated — milestone-level merge is now always used. Remove this setting.");
     }
+    // #4765 — collapse cadence + milestone resquash
+    if (g.collapse_cadence !== undefined) {
+      const validCadence = new Set(["milestone", "slice"]);
+      if (typeof g.collapse_cadence === "string" && validCadence.has(g.collapse_cadence)) {
+        git.collapse_cadence = g.collapse_cadence as "milestone" | "slice";
+      } else {
+        errors.push("git.collapse_cadence must be one of: milestone, slice");
+      }
+    }
+    if (g.milestone_resquash !== undefined) {
+      if (typeof g.milestone_resquash === "boolean") {
+        git.milestone_resquash = g.milestone_resquash;
+        const cadence = (git.collapse_cadence as string | undefined)
+          ?? (typeof g.collapse_cadence === "string" ? g.collapse_cadence : undefined);
+        if (cadence !== "slice") {
+          warnings.push('git.milestone_resquash is ignored unless git.collapse_cadence is "slice"');
+        }
+      } else {
+        errors.push("git.milestone_resquash must be a boolean");
+      }
+    }
 
     if (Object.keys(git).length > 0) {
       validated.git = git as GitPreferences;

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

@@ -68,13 +68,13 @@ export { resolveAllSkillReferences } from "./preferences-skills.js";
 // These lived in preferences-skills.ts but imported loadEffectiveGSDPreferences
 // back from this file, creating a circular dependency. Moved here since they
 // are trivial wrappers over loadEffectiveGSDPreferences.
-export function resolveSkillDiscoveryMode(): SkillDiscoveryMode {
-  const prefs = loadEffectiveGSDPreferences();
+export function resolveSkillDiscoveryMode(basePath?: string): SkillDiscoveryMode {
+  const prefs = loadEffectiveGSDPreferences(basePath);
   return prefs?.preferences.skill_discovery ?? "suggest";
 }
 
-export function resolveSkillStalenessDays(): number {
-  const prefs = loadEffectiveGSDPreferences();
+export function resolveSkillStalenessDays(basePath?: string): number {
+  const prefs = loadEffectiveGSDPreferences(basePath);
   return prefs?.preferences.skill_staleness_days ?? 60;
 }
 
@@ -109,16 +109,16 @@ function legacyGlobalPreferencesPath(): string {
   return join(homedir(), ".pi", "agent", "gsd-preferences.md");
 }
 
-function projectPreferencesPath(): string {
-  return join(gsdRoot(process.cwd()), "PREFERENCES.md");
+function projectPreferencesPath(basePath: string = process.cwd()): string {
+  return join(gsdRoot(basePath), "PREFERENCES.md");
 }
 // Legacy lowercase files can still exist in older projects. Keep them as a
 // compatibility-only fallback, but route new reads/writes through PREFERENCES.md.
 function legacyGlobalPreferencesPathLowercase(): string {
   return join(gsdHome(), "preferences.md");
 }
-function legacyProjectPreferencesPathLowercase(): string {
-  return join(gsdRoot(process.cwd()), "preferences.md");
+function legacyProjectPreferencesPathLowercase(basePath: string = process.cwd()): string {
+  return join(gsdRoot(basePath), "preferences.md");
 }
 
 export function getGlobalGSDPreferencesPath(): string {
@@ -129,8 +129,8 @@ export function getLegacyGlobalGSDPreferencesPath(): string {
   return legacyGlobalPreferencesPath();
 }
 
-export function getProjectGSDPreferencesPath(): string {
-  return projectPreferencesPath();
+export function getProjectGSDPreferencesPath(basePath?: string): string {
+  return projectPreferencesPath(basePath);
 }
 
 // ─── Loading ────────────────────────────────────────────────────────────────
@@ -141,14 +141,14 @@ export function loadGlobalGSDPreferences(): LoadedGSDPreferences | null {
     ?? loadPreferencesFile(legacyGlobalPreferencesPath(), "global");
 }
 
-export function loadProjectGSDPreferences(): LoadedGSDPreferences | null {
-  return loadPreferencesFile(projectPreferencesPath(), "project")
-    ?? loadPreferencesFile(legacyProjectPreferencesPathLowercase(), "project");
+export function loadProjectGSDPreferences(basePath?: string): LoadedGSDPreferences | null {
+  return loadPreferencesFile(projectPreferencesPath(basePath), "project")
+    ?? loadPreferencesFile(legacyProjectPreferencesPathLowercase(basePath), "project");
 }
 
-export function loadEffectiveGSDPreferences(): LoadedGSDPreferences | null {
+export function loadEffectiveGSDPreferences(basePath?: string): LoadedGSDPreferences | null {
   const globalPreferences = loadGlobalGSDPreferences();
-  const projectPreferences = loadProjectGSDPreferences();
+  const projectPreferences = loadProjectGSDPreferences(basePath);
 
   if (!globalPreferences && !projectPreferences) return null;
 
@@ -603,8 +603,8 @@ export function resolvePreDispatchHooks(): PreDispatchHookConfig[] {
  * Worktree isolation requires explicit opt-in because it depends on git
  * branch infrastructure that must be set up before use.
  */
-export function getIsolationMode(): "none" | "worktree" | "branch" {
-  const prefs = loadEffectiveGSDPreferences()?.preferences?.git;
+export function getIsolationMode(basePath?: string): "none" | "worktree" | "branch" {
+  const prefs = loadEffectiveGSDPreferences(basePath)?.preferences?.git;
   if (prefs?.isolation === "worktree") return "worktree";
   if (prefs?.isolation === "branch") return "branch";
   return "none"; // default — no isolation, work on current branch

package/src/resources/extensions/gsd/prompt-cache-optimizer.ts

@@ -55,6 +55,10 @@ const SEMI_STATIC_LABELS = new Set([
   "prior-summaries",
   "project-context",
   "overrides",
+  // KNOWLEDGE is milestone-scoped (stable within a session), so it belongs
+  // in the cacheable prefix. See issue #4719.
+  "knowledge",
+  "project-knowledge",
 ]);
 
 /** Labels that change per-task */

package/src/resources/extensions/gsd/prompt-loader.ts

@@ -24,6 +24,35 @@ import { fileURLToPath } from "node:url";
 import { homedir } from "node:os";
 import { logWarning } from "./workflow-logger.js";
 
+type ExistsFn = (path: string) => boolean;
+
+function hasRequiredExtensionAssets(rootDir: string, exists: ExistsFn = existsSync): boolean {
+  return (
+    exists(join(rootDir, "prompts")) &&
+    exists(join(rootDir, "templates", "task-summary.md"))
+  );
+}
+
+export function resolveExtensionDirFromCandidates(
+  moduleDir: string,
+  agentGsdDir: string,
+  exists: ExistsFn = existsSync,
+): string {
+  const moduleUsable = hasRequiredExtensionAssets(moduleDir, exists);
+  const agentUsable = hasRequiredExtensionAssets(agentGsdDir, exists);
+
+  // Prefer the user-local extension tree when both are valid. This avoids
+  // leaking npm/global-install paths into prompts on Windows.
+  if (agentUsable) return agentGsdDir;
+  if (moduleUsable) return moduleDir;
+
+  // Degraded fallback: if required template is missing in both locations,
+  // keep previous behavior and prefer whichever still has prompts/.
+  if (exists(join(moduleDir, "prompts"))) return moduleDir;
+  if (exists(join(agentGsdDir, "prompts"))) return agentGsdDir;
+  return moduleDir;
+}
+
 /**
  * Resolve the GSD extension directory.
  *
@@ -36,15 +65,9 @@ import { logWarning } from "./workflow-logger.js";
  */
 function resolveExtensionDir(): string {
   const moduleDir = dirname(fileURLToPath(import.meta.url));
-  if (existsSync(join(moduleDir, "prompts"))) return moduleDir;
-
-  // Fallback: user-local agent directory
   const gsdHome = process.env.GSD_HOME || join(homedir(), ".gsd");
   const agentGsdDir = join(gsdHome, "agent", "extensions", "gsd");
-  if (existsSync(join(agentGsdDir, "prompts"))) return agentGsdDir;
-
-  // Last resort: return the module dir (warmCache will silently handle the miss)
-  return moduleDir;
+  return resolveExtensionDirFromCandidates(moduleDir, agentGsdDir);
 }
 
 const __extensionDir = resolveExtensionDir();

package/src/resources/extensions/gsd/prompts/complete-milestone.md

@@ -10,7 +10,11 @@ Your working directory is `{{workingDirectory}}`. All file reads, writes, and sh
 
 All slices are done. You are closing out the milestone — verifying that the assembled work actually delivers the promised outcome, writing the milestone summary, and updating project state. The milestone summary is the final record. After you finish, the system merges the worktree back to the integration branch. If there are queued milestones, the next one starts its own research → plan → execute cycle from a clean slate — the milestone summary is how it learns what was already built.
 
-All relevant context has been preloaded below — the roadmap, all slice summaries, requirements, decisions, and project context are inlined. Start working immediately without re-reading these files.
+Preloaded context below — the roadmap, compact slice-summary excerpts, requirements, decisions, and project context. **Slice summaries are excerpts, not full files.** They include frontmatter fields, section heads (deviations, known limitations, follow-ups), and short narrative only. When drafting LEARNINGS, the Decision Re-evaluation table, or cross-slice narrative, Read the full slice SUMMARY.md files listed under "On-demand Slice Summaries" — do that selectively as needed, not preemptively.
+
+Start with what the excerpts give you. Read full files when the section heads signal richer context you need.
+
+**On-demand Read ordering:** Complete all slice SUMMARY Reads you need for cross-slice synthesis, the Decision Re-evaluation table, and LEARNINGS **before** calling `gsd_complete_milestone` (step 10). Once that tool runs, the milestone is marked complete in the DB — running out of tool budget between step 10 and the LEARNINGS write (step 12) leaves the milestone committed without its LEARNINGS artifact.
 
 {{inlinedContext}}
 
@@ -59,7 +63,7 @@ Then:
    - `followUps` (string) — Follow-up items for future milestones
    - `deviations` (string) — Deviations from the original plan
 11. Update `.gsd/PROJECT.md`: use the `write` tool with `path: ".gsd/PROJECT.md"` and `content` containing the full updated document reflecting milestone completion and current project state. Do NOT use the `edit` tool for this — PROJECT.md is a full-document refresh.
-12. Extract structured learnings from this milestone and persist them to the cross-session knowledge surfaces. Follow the procedure block immediately below — it writes `{{milestoneId}}-LEARNINGS.md`, appends Patterns and Lessons to `.gsd/KNOWLEDGE.md`, and persists Decisions via the `gsd_save_decision` MCP tool.
+12. Extract structured learnings from this milestone and persist them to the GSD memory store. Follow the procedure block immediately below — it writes `{{milestoneId}}-LEARNINGS.md` as the audit trail and persists Patterns, Lessons, and Decisions via `capture_thought` (categories: pattern, gotcha/convention, architecture). The memory store is the single source of truth for cross-session durable knowledge (ADR-013).
 
 {{extractLearningsSteps}}
 

package/src/resources/extensions/gsd/prompts/complete-slice.md

@@ -29,8 +29,8 @@ Then:
 6. If this slice produced evidence that a requirement changed status (Active → Validated, Active → Deferred, etc.), call `gsd_requirement_update` with the requirement ID, updated `status`, and `validation` evidence. Do NOT write `.gsd/REQUIREMENTS.md` directly — the engine renders it from the database.
 7. Prepare the slice completion content you will pass to `gsd_complete_slice` using the camelCase fields `milestoneId`, `sliceId`, `sliceTitle`, `oneLiner`, `narrative`, `verification`, and `uatContent`. Do **not** manually write `{{sliceSummaryPath}}`. Do **not** manually write `{{sliceUatPath}}` — the DB-backed tool is the canonical write path for both artifacts.
 8. Draft the UAT content you will pass as `uatContent` — a concrete UAT script with real test cases derived from the slice plan and task summaries. Include preconditions, numbered steps with expected outcomes, and edge cases. This must NOT be a placeholder or generic template — tailor every test case to what this slice actually built.
-9. Review task summaries for `key_decisions`. Append any significant decisions to `.gsd/DECISIONS.md` if missing.
-10. Review task summaries for patterns, gotchas, or non-obvious lessons learned. If any would save future agents from repeating investigation or hitting the same issues, append them to `.gsd/KNOWLEDGE.md`. Only add entries that are genuinely useful — don't pad with obvious observations.
+9. Review task summaries for `key_decisions`. For each significant decision, call `capture_thought` with `category: "architecture"` (or `"pattern"`) and a `structuredFields` payload of `{ scope, decision, choice, rationale, made_by: "agent", revisable }`.
+10. Review task summaries for patterns, gotchas, or non-obvious lessons learned. For each one that would save future agents from repeating investigation, call `capture_thought` with the matching category (`gotcha`, `convention`, `pattern`, `environment`). The memory store is the single source of truth (ADR-013); do not append to `.gsd/DECISIONS.md` or `.gsd/KNOWLEDGE.md` directly.
 11. Call `gsd_complete_slice` with the camelCase fields `milestoneId`, `sliceId`, `sliceTitle`, `oneLiner`, `narrative`, `verification`, and `uatContent`, plus any optional enrichment fields you have. Do NOT manually mark the roadmap checkbox — the tool writes to the DB, renders `{{sliceSummaryPath}}` and `{{sliceUatPath}}`, and updates the ROADMAP.md projection automatically.
 12. Do not run git commands — the system commits your changes and handles any merge after this unit succeeds.
 13. Update `.gsd/PROJECT.md` if it exists — refresh current state if needed: use the `write` tool with `path: ".gsd/PROJECT.md"` and `content` containing the full updated document reflecting current project state. Do NOT use the `edit` tool for this — PROJECT.md is a full-document refresh.

package/src/resources/extensions/gsd/prompts/debug-diagnose.md

@@ -18,8 +18,10 @@ Goal semantics:
 ## Instructions
 
 1. Read `.gsd/debug/sessions/{{slug}}.json` for any prior session context.
+1a. Call `memory_query` with keywords from the issue (error text, subsystem, file paths). A prior session may have captured this exact gotcha — finding it now saves the investigation.
 2. Investigate the reported issue in `{{workingDirectory}}`.
 3. Follow the goal constraint above strictly.
 4. When complete, surface a clear summary: what failed, why, and what was done (or what a fix would require for root-cause-only mode).
+5. Once root cause is identified, call `capture_thought` with `category: "gotcha"` so future debug sessions can find it via `memory_query`. Keep the content to 1–3 sentences — the symptom, the root cause, and the fix or guard.
 
 {{skillActivation}}

package/src/resources/extensions/gsd/prompts/discuss-headless.md

@@ -162,7 +162,20 @@ Preserve the specification's exact terminology, emphasis, and specific framing.
 6. For each architectural or pattern decision, call `gsd_decision_save` — the tool auto-assigns IDs and regenerates `.gsd/DECISIONS.md` automatically.
 7. {{commitInstruction}}
 
-After writing the files, say exactly: "Milestone {{milestoneId}} ready." — nothing else. Auto-mode will start automatically.
+### Ready-phrase pre-condition (NON-BYPASSABLE)
+
+Before emitting the ready phrase, verify in the CURRENT turn that you have:
+
+- [ ] Written `.gsd/PROJECT.md` (step 2)
+- [ ] Written `.gsd/REQUIREMENTS.md` (step 3)
+- [ ] Written `{{contextPath}}` (step 4)
+- [ ] Called `gsd_plan_milestone` (step 5)
+
+If ANY box is unchecked, **STOP**. Do NOT emit the ready phrase. Emit the missing tool calls in this same turn. The system detects missing artifacts and will reject premature ready signals — you will be asked again and retries are capped.
+
+Do not announce the ready phrase as something you are "about to" do. Do not narrate "now writing the files" as a substitute for actually writing them. The ready phrase is a post-write signal, not an intent signal.
+
+After completing steps 1–7 above, say exactly: "Milestone {{milestoneId}} ready." — nothing else. Auto-mode will start automatically.
 
 ### Multi-Milestone
 
@@ -234,7 +247,21 @@ For single-milestone projects, do NOT write this file.
 
 7. {{multiMilestoneCommitInstruction}}
 
-After writing the files, say exactly: "Milestone {{milestoneId}} ready." — nothing else. Auto-mode will start automatically.
+### Ready-phrase pre-condition (NON-BYPASSABLE)
+
+Before emitting the ready phrase, verify in the CURRENT turn that you have:
+
+- [ ] Written `.gsd/PROJECT.md`
+- [ ] Written `.gsd/REQUIREMENTS.md`
+- [ ] Written the primary milestone `CONTEXT.md`
+- [ ] Called `gsd_plan_milestone` for the primary milestone
+- [ ] Written `.gsd/DISCUSSION-MANIFEST.json` with `gates_completed === total`
+
+If ANY box is unchecked, **STOP**. Do NOT emit the ready phrase. Emit the missing tool calls in this same turn. The system detects missing artifacts and will reject premature ready signals — you will be asked again and retries are capped.
+
+Do not announce the ready phrase as something you are "about to" do. Do not narrate "now writing the files" as a substitute for actually writing them. The ready phrase is a post-write signal, not an intent signal.
+
+After completing every step above, say exactly: "Milestone {{milestoneId}} ready." — nothing else. Auto-mode will start automatically.
 
 ## Critical Rules
 

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

@@ -339,7 +339,20 @@ These sections are in addition to whatever other context the discussion surfaced
 6. For each architectural or pattern decision made during discussion, call `gsd_decision_save` — the tool auto-assigns IDs and regenerates `.gsd/DECISIONS.md` automatically.
 7. {{commitInstruction}}
 
-After writing the files, say exactly: "Milestone {{milestoneId}} ready." — nothing else. Auto-mode will start automatically.
+### Ready-phrase pre-condition (NON-BYPASSABLE)
+
+Before emitting the ready phrase, verify in the CURRENT turn that you have:
+
+- [ ] Written `.gsd/PROJECT.md` (step 2)
+- [ ] Written `.gsd/REQUIREMENTS.md` (step 3)
+- [ ] Written `{{contextPath}}` (step 4)
+- [ ] Called `gsd_plan_milestone` (step 5)
+
+If ANY box is unchecked, **STOP**. Do NOT emit the ready phrase. Emit the missing tool calls in this same turn. The system detects missing artifacts and will reject premature ready signals — you will be asked again and retries are capped.
+
+Do not announce the ready phrase as something you are "about to" do. Do not narrate "now writing the files" as a substitute for actually writing them. The ready phrase is a post-write signal, not an intent signal.
+
+After completing steps 1–7 above, say exactly: "Milestone {{milestoneId}} ready." — nothing else. Auto-mode will start automatically.
 
 ### Multi-Milestone
 
@@ -418,6 +431,20 @@ For single-milestone projects, do NOT write this file — it is only for multi-m
 
 7. {{multiMilestoneCommitInstruction}}
 
-After writing the files, say exactly: "Milestone M001 ready." — nothing else. Auto-mode will start automatically.
+### Ready-phrase pre-condition (NON-BYPASSABLE)
+
+Before emitting the ready phrase, verify in the CURRENT turn that you have:
+
+- [ ] Written `.gsd/PROJECT.md` (Phase 1)
+- [ ] Written `.gsd/REQUIREMENTS.md` (Phase 1)
+- [ ] Written primary-milestone `CONTEXT.md` (Phase 2)
+- [ ] Called `gsd_plan_milestone` for the primary milestone (Phase 2)
+- [ ] Written `.gsd/DISCUSSION-MANIFEST.json` with `gates_completed === total` (Phase 3)
+
+If ANY box is unchecked, **STOP**. Do NOT emit the ready phrase. Emit the missing tool calls in this same turn. The system detects missing artifacts and will reject premature ready signals — you will be asked again and retries are capped.
+
+Do not announce the ready phrase as something you are "about to" do. Do not narrate "now writing the files" as a substitute for actually writing them. The ready phrase is a post-write signal, not an intent signal.
+
+After completing all phases above, say exactly: "Milestone M001 ready." — nothing else. Auto-mode will start automatically.
 
 {{inlinedTemplates}}

package/src/resources/extensions/gsd/prompts/doctor-heal.md

@@ -7,9 +7,10 @@ Rules:
 2. Read before edit.
 3. Prefer fixing authoritative artifacts over masking warnings.
 4. For missing summaries or UAT files, generate the real artifact from existing slice/task context when possible — do not leave placeholders if you can reconstruct the real content.
-5. After each repair cluster, verify the relevant invariant directly from disk.
-6. When done, rerun `/gsd doctor {{doctorCommandSuffix}}` mentally by ensuring the remaining issue set for this scope is reduced or cleared.
-7. Do NOT query `.gsd/gsd.db` directly via `sqlite3` or `node -e require('better-sqlite3')` — use `gsd_milestone_status` to inspect DB state. Direct access bypasses the WAL connection owned by the engine and can corrupt in-flight writes.
+5. For a missing milestone `CONTEXT.md` when the milestone is already past `pre-planning` (phase is `executing`, `summarizing`, `validating-milestone`, or `completing-milestone`): the artifact was skipped during bootstrap and must be reconstructed before execution can resume. Read `PROJECT.md`, `REQUIREMENTS.md`, the milestone's `ROADMAP.md`, and any slice-level context on disk, then write `.gsd/milestones/<milestone-id>/<milestone-id>-CONTEXT.md` with the real context for the scoped milestone. Do not leave a stub — the plan gate will reject it on the next cycle.
+6. After each repair cluster, verify the relevant invariant directly from disk.
+7. When done, rerun `/gsd doctor {{doctorCommandSuffix}}` mentally by ensuring the remaining issue set for this scope is reduced or cleared.
+8. Do NOT query `.gsd/gsd.db` directly via `sqlite3` or `node -e require('better-sqlite3')` — use `gsd_milestone_status` to inspect DB state. Direct access bypasses the WAL connection owned by the engine and can corrupt in-flight writes.
 
 ## Doctor Summary
 
@@ -27,4 +28,4 @@ Then:
 - Repair the unresolved issues in scope
 - Keep changes minimal and targeted
 - If unresolved issues remain outside scope, leave them untouched and mention them briefly
-- End with: "GSD doctor heal complete."
+- End with: "GSD doctor heal complete."

package/src/resources/extensions/gsd/prompts/execute-task.md

@@ -32,6 +32,7 @@ A researcher explored the codebase and a planner decomposed the work — you are
 
 Then:
 0. Narrate step transitions, key implementation decisions, and verification outcomes as you work. Keep it terse — one line between tool-call clusters, not between every call — but write complete sentences in user-facing prose, not shorthand notes or scratchpad fragments.
+0a. Call `memory_query` with 2-4 keywords drawn from the task title and the files it touches. Surface any prior gotchas, conventions, or architectural decisions before you start changing code. Skip only if the task is trivially mechanical.
 1. {{skillActivation}} Follow any activated skills before writing code. If no skills match this task, skip this step.
 2. Execute the steps in the inlined task plan, adapting minor local mismatches when the surrounding code differs from the planner's snapshot
 3. Before any `Write` that creates an artifact or output file, check whether that path already exists. If it does, read it first and decide whether the work is already done, should be extended, or truly needs replacement. "Create" in the plan does **not** mean the file is missing — a prior session may already have started it.
@@ -81,8 +82,8 @@ Then:
     **Scope:** Escalation is instrumented only in `execute-task`. Refine-slice escalation is deferred. Reactive-execute batches run to completion before escalations are surfaced — the dispatch pause happens on the next loop iteration, not mid-batch.
 
     The `escalation` payload is ignored unless `phases.mid_execution_escalation` is enabled; populate it anyway for audit logs.
-17. If you made an architectural, pattern, library, or observability decision during this task that downstream work should know about, append it to `.gsd/DECISIONS.md` (read the template at `~/.gsd/agent/extensions/gsd/templates/decisions.md` if the file doesn't exist yet). Not every task produces decisions — only append when a meaningful choice was made.
-18. If you discover a non-obvious rule, recurring gotcha, or useful pattern during execution, append it to `.gsd/KNOWLEDGE.md`. Only add entries that would save future agents from repeating your investigation. Don't add obvious things.
+17. If you made an architectural, pattern, library, or observability decision during this task that downstream work should know about, call `capture_thought` with `category: "architecture"` (or `"pattern"`). For decisions, populate `structuredFields` with `{ scope, decision, choice, rationale, made_by: "agent", revisable }` so future projection back to a human-visible decisions register stays lossless. Not every task produces decisions — only capture when a meaningful choice was made.
+18. If you discover a non-obvious rule, recurring gotcha, or useful pattern during execution, call `capture_thought` with `category: "gotcha"`, `"convention"`, `"pattern"`, or `"environment"` as appropriate. Only capture entries that would save future agents from repeating your investigation — don't capture obvious things. The memory store is the single source of truth for cross-session knowledge (ADR-013); do not append to `.gsd/DECISIONS.md` or `.gsd/KNOWLEDGE.md` directly.
 19. Read the template at `~/.gsd/agent/extensions/gsd/templates/task-summary.md`
 20. Use that template to prepare the completion content you will pass to `gsd_complete_task` using the camelCase fields `milestoneId`, `sliceId`, `taskId`, `oneLiner`, `narrative`, `verification`, and `verificationEvidence`. Do **not** manually write `{{taskSummaryPath}}` — the DB-backed tool is the canonical write path and renders the summary file for you.
 21. Call `gsd_complete_task` with milestoneId, sliceId, taskId, and the completion fields derived from the template. This is your final required step — do NOT manually edit PLAN.md checkboxes. The tool marks the task complete, updates the DB, renders `{{taskSummaryPath}}`, and updates PLAN.md automatically.