gsd-pi 2.76.0 → 2.77.0

package/dist/resources/extensions/gsd/exec-sandbox.js

@@ -0,0 +1,258 @@
+// GSD Exec Sandbox — tool-output sandboxing for sub-sessions.
+//
+// Runs a script in a subprocess and persists stdout/stderr to
+// `.gsd/exec/<id>.{stdout,stderr,meta.json}`. Only a short digest is
+// returned to the calling agent's context, keeping large outputs
+// (e.g. Playwright snapshots, issue dumps) out of the window.
+//
+// Inspired by mksglu/context-mode (Elastic License 2.0). Independent
+// implementation — no upstream code incorporated.
+import { spawn } from "node:child_process";
+import { existsSync, mkdirSync, writeFileSync } from "node:fs";
+import { randomUUID } from "node:crypto";
+import { resolve } from "node:path";
+const ALWAYS_FORWARD_ENV = ["PATH", "HOME"];
+export const EXEC_DEFAULTS = {
+    clampTimeoutMs: 600_000,
+    defaultTimeoutMs: 30_000,
+    stdoutCapBytes: 1_048_576,
+    stderrCapBytes: 262_144,
+    digestChars: 300,
+    envAllowlist: [
+        "LANG",
+        "LC_ALL",
+        "TERM",
+        "TZ",
+        "SHELL",
+        "USER",
+        "LOGNAME",
+        "TMPDIR",
+        "NODE_OPTIONS",
+        "PYTHONPATH",
+        "PYTHONIOENCODING",
+    ],
+};
+function buildChildEnv(opts) {
+    const source = opts.env ?? process.env;
+    const out = {};
+    const allowed = new Set([...ALWAYS_FORWARD_ENV, ...opts.env_allowlist]);
+    for (const key of allowed) {
+        const value = source[key];
+        if (typeof value === "string")
+            out[key] = value;
+    }
+    return out;
+}
+function clampTimeout(request, opts) {
+    const requested = typeof request.timeout_ms === "number" && Number.isFinite(request.timeout_ms)
+        ? Math.floor(request.timeout_ms)
+        : opts.default_timeout_ms;
+    if (requested < 1)
+        return 1;
+    if (requested > opts.clamp_timeout_ms)
+        return opts.clamp_timeout_ms;
+    return requested;
+}
+function resolveCommand(runtime) {
+    switch (runtime) {
+        case "bash":
+            return { cmd: "bash", args: ["-c"] };
+        case "node":
+            return { cmd: process.execPath, args: ["-e"] };
+        case "python":
+            return { cmd: "python3", args: ["-c"] };
+    }
+}
+function tail(buf, chars) {
+    if (chars <= 0)
+        return "";
+    const text = buf.toString("utf-8");
+    return text.length <= chars ? text : text.slice(text.length - chars);
+}
+/**
+ * Run a script in a subprocess, capture stdout/stderr to files under
+ * `.gsd/exec/<id>.{stdout,stderr,meta.json}`, and return an `ExecSandboxResult`
+ * containing the digest plus metadata.
+ *
+ * Errors from spawn failures resolve (not reject) with `exit_code=null`.
+ * The function is pure with respect to its inputs — no global state beyond
+ * filesystem writes under `baseDir`.
+ */
+export function runExecSandbox(request, opts) {
+    return new Promise((resolveP) => {
+        const id = (opts.generateId ?? defaultGenerateId)();
+        const now = (opts.now ?? (() => new Date()))();
+        const execDir = resolve(opts.baseDir, ".gsd", "exec");
+        if (!existsSync(execDir))
+            mkdirSync(execDir, { recursive: true });
+        const stdoutPath = resolve(execDir, `${id}.stdout`);
+        const stderrPath = resolve(execDir, `${id}.stderr`);
+        const metaPath = resolve(execDir, `${id}.meta.json`);
+        const timeoutMs = clampTimeout(request, opts);
+        const { cmd, args } = resolveCommand(request.runtime);
+        const env = buildChildEnv(opts);
+        const useProcessGroup = process.platform !== "win32";
+        const started = Date.now();
+        let child;
+        try {
+            child = spawn(cmd, [...args, request.script], {
+                cwd: opts.baseDir,
+                env,
+                stdio: ["ignore", "pipe", "pipe"],
+                ...(useProcessGroup ? { detached: true } : {}),
+            });
+        }
+        catch (err) {
+            const duration = Date.now() - started;
+            const message = err instanceof Error ? err.message : String(err);
+            writeFileSync(stdoutPath, "");
+            writeFileSync(stderrPath, `spawn error: ${message}\n`);
+            const result = {
+                id,
+                runtime: request.runtime,
+                exit_code: null,
+                signal: null,
+                timed_out: false,
+                duration_ms: duration,
+                stdout_bytes: 0,
+                stderr_bytes: Buffer.byteLength(`spawn error: ${message}\n`),
+                stdout_truncated: false,
+                stderr_truncated: false,
+                stdout_path: stdoutPath,
+                stderr_path: stderrPath,
+                meta_path: metaPath,
+                digest: `[spawn error: ${message}]`,
+            };
+            writeMeta(metaPath, result, request, now);
+            resolveP(result);
+            return;
+        }
+        const stdoutChunks = [];
+        const stderrChunks = [];
+        let stdoutBytes = 0;
+        let stderrBytes = 0;
+        let stdoutTruncated = false;
+        let stderrTruncated = false;
+        child.stdout?.on("data", (chunk) => {
+            const remaining = opts.stdout_cap_bytes - stdoutBytes;
+            if (remaining <= 0) {
+                stdoutTruncated = true;
+                return;
+            }
+            if (chunk.length <= remaining) {
+                stdoutChunks.push(chunk);
+                stdoutBytes += chunk.length;
+            }
+            else {
+                stdoutChunks.push(chunk.subarray(0, remaining));
+                stdoutBytes += remaining;
+                stdoutTruncated = true;
+            }
+        });
+        child.stderr?.on("data", (chunk) => {
+            const remaining = opts.stderr_cap_bytes - stderrBytes;
+            if (remaining <= 0) {
+                stderrTruncated = true;
+                return;
+            }
+            if (chunk.length <= remaining) {
+                stderrChunks.push(chunk);
+                stderrBytes += chunk.length;
+            }
+            else {
+                stderrChunks.push(chunk.subarray(0, remaining));
+                stderrBytes += remaining;
+                stderrTruncated = true;
+            }
+        });
+        let timedOut = false;
+        const timer = setTimeout(() => {
+            timedOut = true;
+            if (useProcessGroup && child.pid != null) {
+                try {
+                    process.kill(-child.pid, "SIGKILL");
+                }
+                catch {
+                    child.kill("SIGKILL");
+                }
+            }
+            else {
+                child.kill("SIGKILL");
+            }
+        }, timeoutMs);
+        timer.unref?.();
+        const finalize = (exitCode, signal) => {
+            clearTimeout(timer);
+            const duration = Date.now() - started;
+            const stdoutBuf = Buffer.concat(stdoutChunks);
+            const stderrBuf = Buffer.concat(stderrChunks);
+            const stdoutSuffix = stdoutTruncated ? "\n[truncated: stdout cap reached]\n" : "";
+            const stderrSuffix = stderrTruncated ? "\n[truncated: stderr cap reached]\n" : "";
+            writeFileSync(stdoutPath, Buffer.concat([stdoutBuf, Buffer.from(stdoutSuffix, "utf-8")]));
+            writeFileSync(stderrPath, Buffer.concat([stderrBuf, Buffer.from(stderrSuffix, "utf-8")]));
+            const digestBody = tail(stdoutBuf, opts.digest_chars);
+            const digest = digestBody.length > 0
+                ? digestBody
+                : timedOut
+                    ? "[no stdout — timed out]"
+                    : stderrBuf.length > 0
+                        ? `[no stdout — tail of stderr]\n${tail(stderrBuf, opts.digest_chars)}`
+                        : "[no output]";
+            const result = {
+                id,
+                runtime: request.runtime,
+                exit_code: exitCode,
+                signal,
+                timed_out: timedOut,
+                duration_ms: duration,
+                stdout_bytes: stdoutBytes,
+                stderr_bytes: stderrBytes,
+                stdout_truncated: stdoutTruncated,
+                stderr_truncated: stderrTruncated,
+                stdout_path: stdoutPath,
+                stderr_path: stderrPath,
+                meta_path: metaPath,
+                digest,
+            };
+            writeMeta(metaPath, result, request, now);
+            resolveP(result);
+        };
+        child.on("error", (err) => {
+            const message = err instanceof Error ? err.message : String(err);
+            const line = `child error: ${message}\n`;
+            const remaining = opts.stderr_cap_bytes - stderrBytes;
+            if (remaining > 0) {
+                const chunk = Buffer.from(line, "utf-8").subarray(0, remaining);
+                stderrChunks.push(chunk);
+                stderrBytes += chunk.length;
+                if (chunk.length < Buffer.byteLength(line, "utf-8"))
+                    stderrTruncated = true;
+            }
+        });
+        child.on("close", (code, signal) => finalize(code, signal));
+    });
+}
+function defaultGenerateId() {
+    return randomUUID();
+}
+function writeMeta(path, result, request, now) {
+    const meta = {
+        id: result.id,
+        runtime: result.runtime,
+        purpose: request.purpose ?? null,
+        script_chars: request.script.length,
+        started_at: now.toISOString(),
+        finished_at: new Date(now.getTime() + result.duration_ms).toISOString(),
+        exit_code: result.exit_code,
+        signal: result.signal,
+        timed_out: result.timed_out,
+        duration_ms: result.duration_ms,
+        stdout_bytes: result.stdout_bytes,
+        stderr_bytes: result.stderr_bytes,
+        stdout_truncated: result.stdout_truncated,
+        stderr_truncated: result.stderr_truncated,
+        stdout_path: result.stdout_path,
+        stderr_path: result.stderr_path,
+    };
+    writeFileSync(path, `${JSON.stringify(meta, null, 2)}\n`);
+}

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

@@ -45,6 +45,7 @@ const BASELINE_PATTERNS = [
     // ── GSD state directory (symlink to external storage) ──
     ".gsd",
     ".gsd-id",
+    ".mcp.json",
     ".bg-shell/",
     // ── OS junk ──
     ".DS_Store",

package/dist/resources/extensions/gsd/gsd-db.js

@@ -135,7 +135,7 @@ function openRawDb(path) {
     const Database = providerModule;
     return new Database(path);
 }
-const SCHEMA_VERSION = 20;
+const SCHEMA_VERSION = 22;
 function indexExists(db, name) {
     return !!db.prepare("SELECT 1 as present FROM sqlite_master WHERE type = 'index' AND name = ?").get(name);
 }
@@ -234,7 +234,8 @@ function initSchema(db, fileBacked) {
         superseded_by TEXT DEFAULT NULL,
         hit_count INTEGER NOT NULL DEFAULT 0,
         scope TEXT NOT NULL DEFAULT 'project',
-        tags TEXT NOT NULL DEFAULT '[]'
+        tags TEXT NOT NULL DEFAULT '[]',
+        structured_fields TEXT DEFAULT NULL
       )
     `);
         db.exec(`
@@ -490,11 +491,6 @@ function initSchema(db, fileBacked) {
       )
     `);
         db.exec("CREATE INDEX IF NOT EXISTS idx_memories_active ON memories(superseded_by)");
-        db.exec("CREATE INDEX IF NOT EXISTS idx_memories_scope ON memories(scope)");
-        db.exec("CREATE INDEX IF NOT EXISTS idx_memory_sources_kind ON memory_sources(kind)");
-        db.exec("CREATE INDEX IF NOT EXISTS idx_memory_sources_scope ON memory_sources(scope)");
-        db.exec("CREATE INDEX IF NOT EXISTS idx_memory_relations_from ON memory_relations(from_id)");
-        db.exec("CREATE INDEX IF NOT EXISTS idx_memory_relations_to ON memory_relations(to_id)");
         db.exec("CREATE INDEX IF NOT EXISTS idx_replan_history_milestone ON replan_history(milestone_id, created_at)");
         // v13 indexes — hot-path dispatch queries
         db.exec("CREATE INDEX IF NOT EXISTS idx_tasks_active ON tasks(milestone_id, slice_id, status)");
@@ -510,14 +506,21 @@ function initSchema(db, fileBacked) {
         db.exec("CREATE INDEX IF NOT EXISTS idx_turn_git_tx_turn ON turn_git_transactions(trace_id, turn_id)");
         db.exec("CREATE INDEX IF NOT EXISTS idx_audit_events_trace ON audit_events(trace_id, ts)");
         db.exec("CREATE INDEX IF NOT EXISTS idx_audit_events_turn ON audit_events(trace_id, turn_id, ts)");
-        // ADR-011 Phase 2 — also created by the v17 migration; fresh installs
-        // skip migrations so the index must be created here too.
-        db.exec("CREATE INDEX IF NOT EXISTS idx_tasks_escalation_pending ON tasks(milestone_id, slice_id, escalation_pending)");
         db.exec(`CREATE VIEW IF NOT EXISTS active_decisions AS SELECT * FROM decisions WHERE superseded_by IS NULL`);
         db.exec(`CREATE VIEW IF NOT EXISTS active_requirements AS SELECT * FROM requirements WHERE superseded_by IS NULL`);
         db.exec(`CREATE VIEW IF NOT EXISTS active_memories AS SELECT * FROM memories WHERE superseded_by IS NULL`);
         const existing = db.prepare("SELECT count(*) as cnt FROM schema_version").get();
         if (existing && existing["cnt"] === 0) {
+            // Fresh install — all tables are created above with the full current schema,
+            // so it is safe to create all migration-specific indexes here.  For existing
+            // databases these indexes are created inside the individual migration guards
+            // in migrateSchema() after the corresponding columns have been added.
+            db.exec("CREATE INDEX IF NOT EXISTS idx_tasks_escalation_pending ON tasks(milestone_id, slice_id, escalation_pending)");
+            db.exec("CREATE INDEX IF NOT EXISTS idx_memories_scope ON memories(scope)");
+            db.exec("CREATE INDEX IF NOT EXISTS idx_memory_sources_kind ON memory_sources(kind)");
+            db.exec("CREATE INDEX IF NOT EXISTS idx_memory_sources_scope ON memory_sources(scope)");
+            db.exec("CREATE INDEX IF NOT EXISTS idx_memory_relations_from ON memory_relations(from_id)");
+            db.exec("CREATE INDEX IF NOT EXISTS idx_memory_relations_to ON memory_relations(to_id)");
             db.prepare("INSERT INTO schema_version (version, applied_at) VALUES (:version, :applied_at)").run({
                 ":version": SCHEMA_VERSION,
                 ":applied_at": new Date().toISOString(),
@@ -842,19 +845,24 @@ function migrateSchema(db) {
             });
         }
         if (currentVersion < 12) {
+            // NOTE: The original DDL used COALESCE(task_id, '') in the PRIMARY KEY
+            // expression, which is invalid SQLite syntax and causes startup errors on
+            // DBs that migrate through v12. The corrected DDL uses
+            // task_id TEXT NOT NULL DEFAULT '' with a plain column list PK. DBs that
+            // were created with the broken DDL are repaired by the v22 migration below.
             db.exec(`
         CREATE TABLE IF NOT EXISTS quality_gates (
           milestone_id TEXT NOT NULL,
           slice_id TEXT NOT NULL,
           gate_id TEXT NOT NULL,
           scope TEXT NOT NULL DEFAULT 'slice',
-          task_id TEXT DEFAULT NULL,
+          task_id TEXT NOT NULL DEFAULT '',
           status TEXT NOT NULL DEFAULT 'pending',
           verdict TEXT NOT NULL DEFAULT '',
           rationale TEXT NOT NULL DEFAULT '',
           findings TEXT NOT NULL DEFAULT '',
           evaluated_at TEXT DEFAULT NULL,
-          PRIMARY KEY (milestone_id, slice_id, gate_id, COALESCE(task_id, '')),
+          PRIMARY KEY (milestone_id, slice_id, gate_id, task_id),
           FOREIGN KEY (milestone_id, slice_id) REFERENCES slices(milestone_id, id)
         )
       `);
@@ -1006,6 +1014,10 @@ function migrateSchema(db) {
           tags TEXT NOT NULL DEFAULT '[]'
         )
       `);
+            // If memory_sources already existed before v18 (created by an earlier
+            // version of initSchema that lacked scope/tags), add the missing columns.
+            ensureColumn(db, "memory_sources", "scope", `ALTER TABLE memory_sources ADD COLUMN scope TEXT NOT NULL DEFAULT 'project'`);
+            ensureColumn(db, "memory_sources", "tags", `ALTER TABLE memory_sources ADD COLUMN tags TEXT NOT NULL DEFAULT '[]'`);
             db.exec("CREATE INDEX IF NOT EXISTS idx_memories_scope ON memories(scope)");
             db.exec("CREATE INDEX IF NOT EXISTS idx_memory_sources_kind ON memory_sources(kind)");
             db.exec("CREATE INDEX IF NOT EXISTS idx_memory_sources_scope ON memory_sources(scope)");
@@ -1059,6 +1071,65 @@ function migrateSchema(db) {
                 ":applied_at": new Date().toISOString(),
             });
         }
+        if (currentVersion < 21) {
+            // ADR-013 Step 2: preserve structured fields (gsd_save_decision's
+            // scope/decision/choice/rationale/made_by/revisable) on memories rows so
+            // the eventual decisions->memories cutover does not lose schema fidelity.
+            // Nullable JSON column — existing rows stay NULL until backfilled in Step 5.
+            // Use ensureColumn for race-safety (matches v15-v18 pattern; bare ALTER
+            // throws "duplicate column" on the loser of a concurrent open race even
+            // though the transaction wrapper protects the schema_version row).
+            ensureColumn(db, "memories", "structured_fields", "ALTER TABLE memories ADD COLUMN structured_fields TEXT DEFAULT NULL");
+            db.prepare("INSERT INTO schema_version (version, applied_at) VALUES (:version, :applied_at)").run({
+                ":version": 21,
+                ":applied_at": new Date().toISOString(),
+            });
+        }
+        if (currentVersion < 22) {
+            // v22: Repair quality_gates tables that were created by the broken v12
+            // migration (which used COALESCE(task_id, '') as a PK expression — invalid
+            // SQLite DDL). Those DBs have task_id nullable (dflt_value NULL, notnull 0).
+            // Rebuild the table with the correct schema, migrating existing rows via
+            // COALESCE so no data is lost.
+            const qgInfo = db.prepare("PRAGMA table_info(quality_gates)").all();
+            const taskIdCol = qgInfo.find((r) => r["name"] === "task_id");
+            const needsRepair = taskIdCol && (taskIdCol["notnull"] === 0 || taskIdCol["notnull"] === "0");
+            if (needsRepair) {
+                db.exec(`
+          CREATE TABLE quality_gates_new (
+            milestone_id TEXT NOT NULL,
+            slice_id TEXT NOT NULL,
+            gate_id TEXT NOT NULL,
+            scope TEXT NOT NULL DEFAULT 'slice',
+            task_id TEXT NOT NULL DEFAULT '',
+            status TEXT NOT NULL DEFAULT 'pending',
+            verdict TEXT NOT NULL DEFAULT '',
+            rationale TEXT NOT NULL DEFAULT '',
+            findings TEXT NOT NULL DEFAULT '',
+            evaluated_at TEXT DEFAULT NULL,
+            PRIMARY KEY (milestone_id, slice_id, gate_id, task_id),
+            FOREIGN KEY (milestone_id, slice_id) REFERENCES slices(milestone_id, id)
+          )
+        `);
+                db.exec(`
+          INSERT OR IGNORE INTO quality_gates_new
+            (milestone_id, slice_id, gate_id, scope, task_id, status, verdict, rationale, findings, evaluated_at)
+          SELECT milestone_id, slice_id, gate_id, scope, COALESCE(task_id, ''), status, verdict, rationale, findings, evaluated_at
+          FROM quality_gates
+        `);
+                db.exec("DROP TABLE quality_gates");
+                db.exec("ALTER TABLE quality_gates_new RENAME TO quality_gates");
+                db.exec("CREATE INDEX IF NOT EXISTS idx_quality_gates_pending ON quality_gates(milestone_id, slice_id, status)");
+            }
+            // Ensure scope column exists on quality_gates and assessments (guard
+            // against DBs that somehow lack it after a partial migration).
+            ensureColumn(db, "quality_gates", "scope", "ALTER TABLE quality_gates ADD COLUMN scope TEXT NOT NULL DEFAULT 'slice'");
+            ensureColumn(db, "assessments", "scope", "ALTER TABLE assessments ADD COLUMN scope TEXT NOT NULL DEFAULT ''");
+            db.prepare("INSERT INTO schema_version (version, applied_at) VALUES (:version, :applied_at)").run({
+                ":version": 22,
+                ":applied_at": new Date().toISOString(),
+            });
+        }
         db.exec("COMMIT");
     }
     catch (err) {
@@ -1071,6 +1142,8 @@ let currentPath = null;
 let currentPid = 0;
 let _exitHandlerRegistered = false;
 let _dbOpenAttempted = false;
+let _lastDbError = null;
+let _lastDbPhase = null;
 export function getDbProvider() {
     loadProvider();
     return providerName;
@@ -1087,13 +1160,54 @@ export function isDbAvailable() {
 export function wasDbOpenAttempted() {
     return _dbOpenAttempted;
 }
+export function getDbStatus() {
+    loadProvider();
+    return {
+        available: currentDb !== null,
+        provider: providerName,
+        attempted: _dbOpenAttempted,
+        lastError: _lastDbError,
+        lastPhase: _lastDbPhase,
+    };
+}
 export function openDatabase(path) {
     _dbOpenAttempted = true;
     if (currentDb && currentPath !== path)
         closeDatabase();
     if (currentDb && currentPath === path)
         return true;
-    const rawDb = openRawDb(path);
+    // Reset error state only when a new open attempt is actually going to run.
+    _lastDbError = null;
+    _lastDbPhase = null;
+    let rawDb;
+    let fallbackProvider = null;
+    let fallbackModule = null;
+    try {
+        rawDb = openRawDb(path);
+    }
+    catch (primaryErr) {
+        _lastDbPhase = "open";
+        _lastDbError = primaryErr instanceof Error ? primaryErr : new Error(String(primaryErr));
+        // node:sqlite loaded but failed to open this file — try better-sqlite3 as fallback.
+        if (providerName === "node:sqlite") {
+            try {
+                const mod = _require("better-sqlite3");
+                const Db = (mod && mod.default) ? mod.default : mod;
+                if (typeof Db === "function") {
+                    rawDb = new Db(path);
+                    fallbackProvider = "better-sqlite3";
+                    fallbackModule = Db;
+                    _lastDbError = null;
+                    _lastDbPhase = null;
+                }
+            }
+            catch {
+                // fallback unavailable; surface original error
+            }
+        }
+        if (!rawDb)
+            throw primaryErr;
+    }
     if (!rawDb)
         return false;
     const adapter = createAdapter(rawDb);
@@ -1111,6 +1225,8 @@ export function openDatabase(path) {
                 process.stderr.write("gsd-db: recovered corrupt database via VACUUM\n");
             }
             catch (retryErr) {
+                _lastDbPhase = "vacuum-recovery";
+                _lastDbError = retryErr instanceof Error ? retryErr : new Error(String(retryErr));
                 try {
                     adapter.close();
                 }
@@ -1121,15 +1237,22 @@ export function openDatabase(path) {
             }
         }
         else {
+            _lastDbPhase = "initSchema";
+            _lastDbError = err instanceof Error ? err : new Error(String(err));
             try {
                 adapter.close();
             }
             catch (e) {
-                logWarning("db", `close after VACUUM failed: ${e.message}`);
+                logWarning("db", `close after initSchema failed: ${e.message}`);
             }
             throw err;
         }
     }
+    // Commit fallback provider switch only after open + schema both succeeded.
+    if (fallbackProvider) {
+        providerName = fallbackProvider;
+        providerModule = fallbackModule;
+    }
     currentDb = adapter;
     currentPath = path;
     currentPid = process.pid;
@@ -1168,8 +1291,12 @@ export function closeDatabase() {
         currentDb = null;
         currentPath = null;
         currentPid = 0;
-        _dbOpenAttempted = false;
     }
+    // Reset session-scoped state unconditionally so stale error info from a
+    // failed open doesn't persist into the next open attempt or status check.
+    _dbOpenAttempted = false;
+    _lastDbError = null;
+    _lastDbPhase = null;
 }
 /** Run a full VACUUM — call sparingly (e.g. after milestone completion). */
 export function vacuumDatabase() {
@@ -2269,7 +2396,10 @@ export function reconcileWorktreeDb(mainDbPath, worktreeDbPath) {
           SELECT path, artifact_type, milestone_id, slice_id, task_id, full_content, imported_at
           FROM wt.artifacts
         `).run());
-                // Merge milestones — worktree may have updated status/planning fields
+                // Merge milestones — worktree may have updated status/planning fields.
+                // Never downgrade status: complete > active > pre-planning (#4372).
+                // A stale worktree may carry an older 'active' status for a milestone
+                // that the main DB has already marked 'complete'; preserve the higher status.
                 merged.milestones = countChanges(adapter.prepare(`
           INSERT OR REPLACE INTO milestones (
             id, title, status, depends_on, created_at, completed_at,
@@ -2277,11 +2407,25 @@ export function reconcileWorktreeDb(mainDbPath, worktreeDbPath) {
             verification_contract, verification_integration, verification_operational, verification_uat,
             definition_of_done, requirement_coverage, boundary_map_markdown
           )
-          SELECT id, title, status, depends_on, created_at, completed_at,
-                 vision, success_criteria, key_risks, proof_strategy,
-                 verification_contract, verification_integration, verification_operational, verification_uat,
-                 definition_of_done, requirement_coverage, boundary_map_markdown
-          FROM wt.milestones
+          SELECT w.id, w.title,
+                 CASE
+                   WHEN m.status IN ('complete', 'done') AND w.status NOT IN ('complete', 'done')
+                   THEN m.status ELSE w.status
+                 END,
+                 w.depends_on,
+                 CASE
+                   WHEN m.status IN ('complete', 'done') AND w.status NOT IN ('complete', 'done')
+                   THEN m.created_at ELSE w.created_at
+                 END,
+                 CASE
+                   WHEN m.status IN ('complete', 'done') AND w.status NOT IN ('complete', 'done')
+                   THEN m.completed_at ELSE w.completed_at
+                 END,
+                 w.vision, w.success_criteria, w.key_risks, w.proof_strategy,
+                 w.verification_contract, w.verification_integration, w.verification_operational, w.verification_uat,
+                 w.definition_of_done, w.requirement_coverage, w.boundary_map_markdown
+          FROM wt.milestones w
+          LEFT JOIN milestones m ON m.id = w.id
         `).run());
                 // Merge slices — preserve worktree progress but never downgrade completed status (#2558).
                 // ADR-011 Phase 1: carry is_sketch + sketch_scope so reconcile doesn't
@@ -2948,8 +3092,8 @@ export function bulkInsertLegacyHierarchy(payload) {
 export function insertMemoryRow(args) {
     if (!currentDb)
         throw new GSDError(GSD_STALE_STATE, "gsd-db: No database open");
-    currentDb.prepare(`INSERT INTO memories (id, category, content, confidence, source_unit_type, source_unit_id, created_at, updated_at, scope, tags)
-     VALUES (:id, :category, :content, :confidence, :source_unit_type, :source_unit_id, :created_at, :updated_at, :scope, :tags)`).run({
+    currentDb.prepare(`INSERT INTO memories (id, category, content, confidence, source_unit_type, source_unit_id, created_at, updated_at, scope, tags, structured_fields)
+     VALUES (:id, :category, :content, :confidence, :source_unit_type, :source_unit_id, :created_at, :updated_at, :scope, :tags, :structured_fields)`).run({
         ":id": args.id,
         ":category": args.category,
         ":content": args.content,
@@ -2960,6 +3104,7 @@ export function insertMemoryRow(args) {
         ":updated_at": args.updatedAt,
         ":scope": args.scope ?? "project",
         ":tags": JSON.stringify(args.tags ?? []),
+        ":structured_fields": args.structuredFields == null ? null : JSON.stringify(args.structuredFields),
     });
 }
 export function insertMemorySourceRow(args) {