@opengsd/gsd-pi 1.8.1 → 1.9.0-dev.97ef11e3

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

@@ -12,7 +12,7 @@
 //   - broadcast queries: WHERE target_worker IS NULL
 // Workers should poll for both forms (their own ID + broadcasts) on each
 // claim cycle.
-import { _getAdapter, isDbAvailable, transaction, } from "../gsd-db.js";
+import { _getAdapter, immediateTransaction, isDbAvailable, transaction, } from "../gsd-db.js";
 /**
  * Enqueue a command. Returns the new row id. Broadcast commands
  * (targetWorker=null) will be claimed by exactly one worker — the IPC
@@ -47,7 +47,12 @@ export function claimNextCommand(workerId) {
         return null;
     const now = new Date().toISOString();
     const db = _getAdapter();
-    return transaction(() => {
+    // BEGIN IMMEDIATE: this is a read-then-write claim. Under WAL, a deferred
+    // transaction that reads first and then upgrades to a writer can fail with
+    // SQLITE_BUSY_SNAPSHOT (not retried by busy_timeout) when two workers race;
+    // taking the write lock up front serializes claimants so the loser waits
+    // and then sees the row already claimed (changes !== 1 → null).
+    return immediateTransaction(() => {
         // Find the oldest unclaimed command targeted at this worker OR
         // broadcast. The partial index covers both via NULL-in-B-tree.
         const row = db.prepare(`SELECT id, target_worker, command, args_json, enqueued_at,

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

@@ -10,7 +10,7 @@
 // writer layer.
 import { createRequire } from "node:module";
 import { existsSync, copyFileSync, mkdirSync, realpathSync } from "node:fs";
-import { dirname, join } from "node:path";
+import { dirname, join, resolve } from "node:path";
 import { GSDError, GSD_STALE_STATE } from "../errors.js";
 import { logError, logWarning } from "../workflow-logger.js";
 import { createDbAdapter } from "../db-adapter.js";
@@ -18,7 +18,7 @@ import { createBaseSchemaObjects } from "../db-base-schema.js";
 import { createCoordinationTablesV24 } from "../db-coordination-schema.js";
 import { createDbConnectionCache } from "../db-connection-cache.js";
 import { backupDatabaseBeforeMigration, isMigrationBackupError } from "../db-migration-backup.js";
-import { applyMigrationV2Artifacts, applyMigrationV3Memories, applyMigrationV4DecisionMadeBy, applyMigrationV5HierarchyTables, applyMigrationV6SliceSummaries, applyMigrationV7Dependencies, applyMigrationV8PlanningFields, applyMigrationV9Ordering, applyMigrationV10ReplanTrigger, applyMigrationV11TaskPlanning, applyMigrationV12QualityGates, applyMigrationV13HotPathIndexes, applyMigrationV14SliceDependencies, applyMigrationV15AuditTables, applyMigrationV16EscalationSource, applyMigrationV17TaskEscalation, applyMigrationV18MemorySources, applyMigrationV19MemoryFts, applyMigrationV20MemoryRelations, applyMigrationV21StructuredMemories, applyMigrationV22QualityGateRepair, applyMigrationV23MilestoneQueue, applyMigrationV26MilestoneCommitAttributions, applyMigrationV27ArtifactHash, applyMigrationV28MemoryLastHitAt, applyMigrationV29RepositoryTargets, } from "../db-migration-steps.js";
+import { applyMigrationV2Artifacts, applyMigrationV3Memories, applyMigrationV4DecisionMadeBy, applyMigrationV5HierarchyTables, applyMigrationV6SliceSummaries, applyMigrationV7Dependencies, applyMigrationV8PlanningFields, applyMigrationV9Ordering, applyMigrationV10ReplanTrigger, applyMigrationV11TaskPlanning, applyMigrationV12QualityGates, applyMigrationV13HotPathIndexes, applyMigrationV14SliceDependencies, applyMigrationV15AuditTables, applyMigrationV16EscalationSource, applyMigrationV17TaskEscalation, applyMigrationV18MemorySources, applyMigrationV19MemoryFts, applyMigrationV20MemoryRelations, applyMigrationV21StructuredMemories, applyMigrationV22QualityGateRepair, applyMigrationV23MilestoneQueue, applyMigrationV26MilestoneCommitAttributions, applyMigrationV27ArtifactHash, applyMigrationV28MemoryLastHitAt, applyMigrationV29RepositoryTargets, applyMigrationV30ReworkBriefs, } from "../db-migration-steps.js";
 import { isMemoriesFtsAvailableSchema, rebuildMemoriesFtsSchemaOnce, tryCreateMemoriesFtsSchema, } from "../db-memory-fts-schema.js";
 import { createDbOpenState } from "../db-open-state.js";
 import { createRuntimeKvTableV25 } from "../db-runtime-kv-schema.js";
@@ -31,7 +31,10 @@ function getGsdRequire() {
     if (_gsdRequire !== undefined)
         return _gsdRequire;
     try {
-        _gsdRequire = createRequire(import.meta.url);
+        // Next.js may emit this module into a CommonJS chunk. Avoid ESM-only module
+        // metadata syntax here; it is a hard parse error there.
+        const packageRoot = process.env.GSD_WEB_PACKAGE_ROOT || process.env.GSD_PKG_ROOT || process.cwd();
+        _gsdRequire = createRequire(resolve(packageRoot, "package.json"));
     }
     catch {
         _gsdRequire = null;
@@ -55,7 +58,7 @@ const providerLoader = createSqliteProviderLoader({
     nodeVersion: process.versions.node,
     writeStderr: (message) => process.stderr.write(message),
 });
-export const SCHEMA_VERSION = 29;
+export const SCHEMA_VERSION = 30;
 function initSchema(db, fileBacked, dbPath) {
     const conservativeFilePragmas = fileBacked && _isLikelyWslDrvFsPathForTest(dbPath);
     if (fileBacked)
@@ -80,19 +83,41 @@ function initSchema(db, fileBacked, dbPath) {
         });
         const existing = db.prepare("SELECT count(*) as cnt FROM schema_version").get();
         if (existing && existing["cnt"] === 0) {
-            createCoordinationTablesV24(db);
-            createRuntimeKvTableV25(db);
-            // 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)");
-            recordSchemaVersion(db, SCHEMA_VERSION);
+            // An empty schema_version table usually means a fresh install, but it can
+            // also be a legacy/truncated DB that already holds user data. Stamping
+            // that DB SCHEMA_VERSION without running migrations would mis-mark it as
+            // fully migrated and break at first query. Probe before stamping.
+            const hasData = ["milestones", "decisions", "memories"].some((t) => {
+                try {
+                    const r = db.prepare(`SELECT count(*) as cnt FROM ${t}`).get();
+                    return (r?.["cnt"] ?? 0) > 0;
+                }
+                catch { /* table absent on a truly fresh DB — treat as no data */
+                    return false;
+                }
+            });
+            if (hasData) {
+                // Legacy DB with data but no version row: record the baseline so
+                // migrateSchema runs the full chain instead of stamping the current version.
+                recordSchemaVersion(db, 1);
+            }
+            else {
+                createCoordinationTablesV24(db);
+                createRuntimeKvTableV25(db);
+                // 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.exec("CREATE INDEX IF NOT EXISTS idx_rework_briefs_task ON rework_briefs(milestone_id, slice_id, task_id)");
+                db.exec("CREATE INDEX IF NOT EXISTS idx_rework_findings_status ON rework_brief_findings(brief_id, severity, status)");
+                recordSchemaVersion(db, SCHEMA_VERSION);
+            }
         }
         db.exec("COMMIT");
     }
@@ -143,9 +168,16 @@ function copyQualityGateRowsToRepairedTable(db) {
     FROM quality_gates
   `);
 }
+let _migrationFaultForTest = false;
+/** Test-only: force migrateSchema to throw after applying its steps but before COMMIT. */
+export function _setMigrationFaultForTest(v) { _migrationFaultForTest = v; }
 function migrateSchema(db, dbPath) {
     const currentVersion = getCurrentSchemaVersion(db);
-    if (currentVersion >= SCHEMA_VERSION)
+    if (currentVersion > SCHEMA_VERSION) {
+        throw new Error(`gsd.db schema is v${currentVersion}, newer than the v${SCHEMA_VERSION} this gsd-pi supports. ` +
+            `Update gsd-pi (npm i -g @opengsd/gsd-pi) before opening this project.`);
+    }
+    if (currentVersion === SCHEMA_VERSION)
         return;
     backupDatabaseBeforeMigration(db, dbPath, currentVersion, {
         existsSync,
@@ -282,6 +314,12 @@ function migrateSchema(db, dbPath) {
             applyMigrationV29RepositoryTargets(db);
             recordSchemaVersion(db, 29);
         }
+        if (currentVersion < 30) {
+            applyMigrationV30ReworkBriefs(db);
+            recordSchemaVersion(db, 30);
+        }
+        if (_migrationFaultForTest)
+            throw new Error("migration fault injected for test");
         db.exec("COMMIT");
     }
     catch (err) {

package/dist/resources/extensions/gsd/db/writers/cascades.js

@@ -172,7 +172,11 @@ export function skipSliceCascade(milestoneId, sliceId) {
             outcome = { ok: false, reason: "slice-not-found" };
             return;
         }
-        if (slice.status === "complete" || slice.status === "done") {
+        // Reject any closed slice except "skipped" (which falls through to the
+        // wasAlreadySkipped no-op). isClosedStatus covers the "closed"/"done"
+        // aliases too — hand-picking literals here nulls a completed slice's
+        // completed_at on re-skip.
+        if (isClosedStatus(slice.status) && slice.status !== "skipped") {
             outcome = { ok: false, reason: "slice-already-complete" };
             return;
         }

package/dist/resources/extensions/gsd/db/writers/status.js

@@ -37,22 +37,29 @@ function requireDb() {
 export function applyStatusTransition(t) {
     const db = requireDb();
     const completedAt = t.completedAt ?? null;
+    const preserve = t.preserveCompletion ? 1 : 0;
     switch (t.entity) {
         case "task":
-            db.prepare(`UPDATE tasks SET status = :status, completed_at = :completed_at
+            db.prepare(`UPDATE tasks SET status = :status,
+           completed_at = CASE WHEN :preserve_completion = 1 AND tasks.completed_at IS NOT NULL
+                               THEN tasks.completed_at ELSE :completed_at END
          WHERE milestone_id = :milestone_id AND slice_id = :slice_id AND id = :id`).run({
                 ":status": t.status,
                 ":completed_at": completedAt,
+                ":preserve_completion": preserve,
                 ":milestone_id": t.milestoneId,
                 ":slice_id": t.sliceId,
                 ":id": t.taskId,
             });
             return;
         case "slice":
-            db.prepare(`UPDATE slices SET status = :status, completed_at = :completed_at
+            db.prepare(`UPDATE slices SET status = :status,
+           completed_at = CASE WHEN :preserve_completion = 1 AND slices.completed_at IS NOT NULL
+                               THEN slices.completed_at ELSE :completed_at END
          WHERE milestone_id = :milestone_id AND id = :id`).run({
                 ":status": t.status,
                 ":completed_at": completedAt,
+                ":preserve_completion": preserve,
                 ":milestone_id": t.milestoneId,
                 ":id": t.sliceId,
             });
@@ -63,7 +70,10 @@ export function applyStatusTransition(t) {
             if (currentStatus && isClosedStatus(currentStatus) && !isClosedStatus(t.status)) {
                 throw new Error(`Cannot update closed milestone ${t.milestoneId} from ${currentStatus} to ${t.status}; use gsd_milestone_reopen for an explicit reopen.`);
             }
-            db.prepare(`UPDATE milestones SET status = :status, completed_at = :completed_at WHERE id = :id`).run({ ":status": t.status, ":completed_at": completedAt, ":id": t.milestoneId });
+            db.prepare(`UPDATE milestones SET status = :status,
+           completed_at = CASE WHEN :preserve_completion = 1 AND milestones.completed_at IS NOT NULL
+                               THEN milestones.completed_at ELSE :completed_at END
+         WHERE id = :id`).run({ ":status": t.status, ":completed_at": completedAt, ":preserve_completion": preserve, ":id": t.milestoneId });
             return;
         }
     }

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

@@ -221,6 +221,32 @@ export function createBaseSchemaObjects(db, hooks) {
       created_at TEXT NOT NULL DEFAULT '',
       FOREIGN KEY (milestone_id) REFERENCES milestones(id)
     )
+  `);
+    db.exec(`
+    CREATE TABLE IF NOT EXISTS rework_briefs (
+      id TEXT PRIMARY KEY,
+      milestone_id TEXT NOT NULL DEFAULT '',
+      slice_id TEXT NOT NULL DEFAULT '',
+      task_id TEXT NOT NULL DEFAULT '',
+      created_at TEXT NOT NULL DEFAULT '',
+      updated_at TEXT NOT NULL DEFAULT ''
+    )
+  `);
+    db.exec(`
+    CREATE TABLE IF NOT EXISTS rework_brief_findings (
+      brief_id TEXT NOT NULL,
+      finding_id TEXT NOT NULL,
+      severity TEXT NOT NULL DEFAULT 'blocking',
+      description TEXT NOT NULL DEFAULT '',
+      required_fix TEXT NOT NULL DEFAULT '',
+      verification_commands TEXT NOT NULL DEFAULT '[]',
+      status TEXT NOT NULL DEFAULT 'pending',
+      evidence TEXT NOT NULL DEFAULT '',
+      decision_ref TEXT NOT NULL DEFAULT '',
+      updated_at TEXT NOT NULL DEFAULT '',
+      PRIMARY KEY (brief_id, finding_id),
+      FOREIGN KEY (brief_id) REFERENCES rework_briefs(id)
+    )
   `);
     db.exec(`
     CREATE TABLE IF NOT EXISTS assessments (
@@ -336,6 +362,8 @@ export function createBaseSchemaObjects(db, hooks) {
   `);
     db.exec("CREATE INDEX IF NOT EXISTS idx_memories_active ON memories(superseded_by)");
     db.exec("CREATE INDEX IF NOT EXISTS idx_replan_history_milestone ON replan_history(milestone_id, created_at)");
+    db.exec("CREATE INDEX IF NOT EXISTS idx_rework_briefs_task ON rework_briefs(milestone_id, slice_id, task_id)");
+    db.exec("CREATE INDEX IF NOT EXISTS idx_rework_findings_status ON rework_brief_findings(brief_id, severity, status)");
     db.exec("CREATE INDEX IF NOT EXISTS idx_tasks_active ON tasks(milestone_id, slice_id, status)");
     db.exec("CREATE INDEX IF NOT EXISTS idx_slices_active ON slices(milestone_id, status)");
     db.exec("CREATE INDEX IF NOT EXISTS idx_milestones_status ON milestones(status)");

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

@@ -418,3 +418,33 @@ export function applyMigrationV22QualityGateRepair(db, hooks) {
     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 ''");
 }
+export function applyMigrationV30ReworkBriefs(db) {
+    db.exec(`
+    CREATE TABLE IF NOT EXISTS rework_briefs (
+      id TEXT PRIMARY KEY,
+      milestone_id TEXT NOT NULL DEFAULT '',
+      slice_id TEXT NOT NULL DEFAULT '',
+      task_id TEXT NOT NULL DEFAULT '',
+      created_at TEXT NOT NULL DEFAULT '',
+      updated_at TEXT NOT NULL DEFAULT ''
+    )
+  `);
+    db.exec(`
+    CREATE TABLE IF NOT EXISTS rework_brief_findings (
+      brief_id TEXT NOT NULL,
+      finding_id TEXT NOT NULL,
+      severity TEXT NOT NULL DEFAULT 'blocking',
+      description TEXT NOT NULL DEFAULT '',
+      required_fix TEXT NOT NULL DEFAULT '',
+      verification_commands TEXT NOT NULL DEFAULT '[]',
+      status TEXT NOT NULL DEFAULT 'pending',
+      evidence TEXT NOT NULL DEFAULT '',
+      decision_ref TEXT NOT NULL DEFAULT '',
+      updated_at TEXT NOT NULL DEFAULT '',
+      PRIMARY KEY (brief_id, finding_id),
+      FOREIGN KEY (brief_id) REFERENCES rework_briefs(id)
+    )
+  `);
+    db.exec("CREATE INDEX IF NOT EXISTS idx_rework_briefs_task ON rework_briefs(milestone_id, slice_id, task_id)");
+    db.exec("CREATE INDEX IF NOT EXISTS idx_rework_findings_status ON rework_brief_findings(brief_id, severity, status)");
+}

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

@@ -12,8 +12,11 @@ export function ensureColumn(db, table, column, ddl) {
         db.exec(ddl);
 }
 export function getCurrentSchemaVersion(db) {
+    // MAX(version) on an empty table returns a row whose value is NULL —
+    // treat that (and any non-numeric value) as version 0, not NULL-as-number.
     const row = db.prepare("SELECT MAX(version) as v FROM schema_version").get();
-    return row ? row["v"] : 0;
+    const v = row?.["v"];
+    return typeof v === "number" ? v : 0;
 }
 export function recordSchemaVersion(db, version) {
     db.prepare("INSERT INTO schema_version (version, applied_at) VALUES (:version, :applied_at)").run({

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

@@ -128,7 +128,7 @@ Diagnostics record the file path, scope (global/project), severity (error/warnin
   - Two equivalent ways to set it: inline as `models.<phase>.thinking`, or as a separate `thinking:` block keyed by phase. For the same phase, the inline value wins over the block; project preferences win over global; a phase that's unset inherits via the same sibling chain as `models` (e.g. `discuss → planning`).
   - If no thinking is configured for a phase, the session level (set via `/model`) is used, exactly as before — this is fully backward-compatible.
   - `execute-task` (code-writing) has a measured reasoning floor of `medium`: at lower levels models stop planning edits and thrash on file re-reads. The floor applies to the session/default path. An **explicit** `execution` thinking level bypasses the floor and is honored verbatim (with a one-time advisory) — set `execution: low` deliberately if you want it.
-  - Levels a model can't support are clamped to the nearest supported level at dispatch and never sent to the provider, so a model/level mismatch never fails a unit mid-run. `xhigh` is only honored by select model families.
+  - Levels a model can't support are clamped to the nearest supported level at dispatch and never sent to the provider, so a model/level mismatch never fails a unit mid-run. `xhigh` support is model-dependent; current examples include OpenAI Codex Max models and Claude Sonnet 5 on Amazon Bedrock.
 
 - `skill_staleness_days`: number — skills unused for this many days get deprioritized during discovery. Set to `0` to disable staleness tracking. Default: `60`.
 
@@ -357,6 +357,28 @@ In `"parent"` mode, slice/task `targetRepositories` default to the declared chil
   - `"replace"` requires `prompt`.
   - `"skip"` is valid with no additional fields.
 
+- `planning_subagents`: object — project-local widening for read-only planning subagent dispatch. Supported unit keys are `plan-milestone` and `plan-slice`; each has:
+  - `allowed`: string[] — additional planning-safe agents for that unit.
+
+  Agents must already be classified by GSD as read-only planning specialists: `mnemo`, `scout`, `planner`, `reviewer`, `security`, or `tester`. The write gate still blocks source writes outside `.gsd/**`, unrestricted bash, stale subagent calls without agent identities, agents outside the global read-only registry, and agents not listed for the active unit.
+
+  Example:
+
+  ```yaml
+  planning_subagents:
+    plan-milestone:
+      allowed:
+        - scout
+        - planner
+        - security
+    plan-slice:
+      allowed:
+        - scout
+        - planner
+        - reviewer
+        - security
+  ```
+
   **Known unit types for `before`/`after`:** `research-milestone`, `plan-milestone`, `research-slice`, `plan-slice`, `execute-task`, `complete-slice`, `replan-slice`, `reassess-roadmap`, `run-uat`.
 
 - `experimental`: opt-in experimental features. All features here are **off by default** — you must explicitly set each one to `true` to enable it. Features in this block may change or be removed without a deprecation cycle while in experimental status. Keys:
@@ -482,13 +504,13 @@ Inline form — thinking pinned alongside the model:
 version: 1
 models:
   planning:
-    model: openai-codex/gpt-5.4
+    model: bedrock/global.anthropic.claude-sonnet-5
     thinking: xhigh
   execution:
-    model: openai-codex/gpt-5.4
+    model: bedrock/global.anthropic.claude-sonnet-5
     thinking: low      # explicit → bypasses the execute-task medium floor
   validation:
-    model: openai-codex/gpt-5.4
+    model: bedrock/global.anthropic.claude-sonnet-5
     thinking: high
 ---
 ```

package/dist/resources/extensions/gsd/doctor-engine-checks.js

@@ -3,7 +3,7 @@ import { isAbsolute, join, relative, sep } from "node:path";
 import { deleteArtifactByPath, getAllMilestones, getMilestoneSlices, getSliceTasks, isDbAvailable, isMemoriesFtsAvailable, repairTaskCompletionFromSummary, _getAdapter, } from "./gsd-db.js";
 import { MEMORIES_FTS_REBUILT_KEY } from "./db-memory-fts-schema.js";
 import { isAfter, latestExplicitReopenAt } from "./milestone-reopen-events.js";
-import { buildTaskFileName, gsdProjectionRoot, gsdRoot, resolveGsdPathContract, resolveMilestoneFile, resolveMilestonePath, resolveSliceFile, } from "./paths.js";
+import { gsdProjectionRoot, gsdRoot, resolveGsdPathContract, resolveMilestoneFile, resolveSliceFile, resolveTaskFile, } from "./paths.js";
 import { deriveState } from "./state.js";
 import { isClosedStatus } from "./status-guards.js";
 import { workflowEventLogPath } from "./workflow-event-ledger.js";
@@ -58,6 +58,23 @@ function reportCheckboxDbStatusDivergence(issues, basePath, filePath, scope, uni
         fixable: false,
     });
 }
+function bareDuplicateMilestoneId(milestoneId) {
+    const match = milestoneId.match(/^(M\d{3})-[a-z0-9]{6}$/i);
+    return match?.[1]?.toUpperCase() ?? null;
+}
+function checkboxDbStatusMilestoneIds(basePath, milestoneIds) {
+    if (!hasFlatPhaseLayout(basePath))
+        return milestoneIds;
+    // Flat-phase directories are keyed by phase number. A restored
+    // M003-xxxxxx row alongside M003 is a stale duplicate for the same
+    // phases/03-* projection, so checking both can compare DB status against two
+    // competing PLAN files and report a persistent false divergence.
+    const allIds = new Set(milestoneIds.map((id) => id.toUpperCase()));
+    return milestoneIds.filter((milestoneId) => {
+        const bareId = bareDuplicateMilestoneId(milestoneId);
+        return !bareId || !allIds.has(bareId);
+    });
+}
 function checkProjectionCheckboxDbStatus(basePath, milestoneIds, issues) {
     for (const milestoneId of milestoneIds) {
         const roadmapPath = resolveMilestoneFile(basePath, milestoneId, "ROADMAP");
@@ -152,11 +169,8 @@ function resolveFlatPhaseArtifactDiskPath(basePath, row) {
     if (!artifactType)
         return null;
     if (row.slice_id && row.task_id) {
-        const phaseDir = resolveMilestonePath(basePath, row.milestone_id);
-        if (!phaseDir || !isFlatPhaseDiskPath(basePath, phaseDir))
-            return null;
-        const candidate = join(phaseDir, buildTaskFileName(row.task_id, artifactType));
-        return existsSync(candidate) ? candidate : null;
+        const candidate = resolveTaskFile(basePath, row.milestone_id, row.slice_id, row.task_id, artifactType);
+        return candidate && isFlatPhaseDiskPath(basePath, candidate) ? candidate : null;
     }
     const candidate = row.slice_id
         ? resolveSliceFile(basePath, row.milestone_id, row.slice_id, artifactType)
@@ -325,7 +339,9 @@ function staleMilestonesArtifactRowFixable(basePath, row, artifactRows) {
 }
 function stalePhasesArtifactRowFixable(basePath, row, artifactRows) {
     const issuePath = artifactPathRelativeToGsd(row.path);
-    return issuePath.startsWith(`${LAYOUT_SEGMENTS.level1}/`) && hasPresentMilestonesReplacement(basePath, row, artifactRows);
+    return issuePath.startsWith(`${LAYOUT_SEGMENTS.level1}/`) &&
+        (hasPresentFlatPhaseReplacement(basePath, row, artifactRows) ||
+            hasPresentMilestonesReplacement(basePath, row, artifactRows));
 }
 function staleArtifactRowFixable(basePath, row, artifactRows) {
     return staleMilestonesArtifactRowFixable(basePath, row, artifactRows) ||
@@ -661,7 +677,7 @@ export async function checkEngineHealth(basePath, issues, fixesApplied, options)
     // block doctor.
     try {
         if (isDbAvailable()) {
-            checkProjectionCheckboxDbStatus(basePath, getAllMilestones().map((milestone) => milestone.id), issues);
+            checkProjectionCheckboxDbStatus(basePath, checkboxDbStatusMilestoneIds(basePath, getAllMilestones().map((milestone) => milestone.id)), issues);
         }
     }
     catch {

package/dist/resources/extensions/gsd/error-classifier.js

@@ -38,8 +38,12 @@ const NETWORK_RE = /network|ECONNRESET|ETIMEDOUT|ECONNREFUSED|socket hang up|web
 // transient errors so auto-mode can retry with reduced budget or fall back to a larger-context model.
 // See: https://github.com/open-gsd/gsd-pi/issues/4528
 const SERVER_RE = /internal(?: server)?[ _-]?error|server[ _-]?error|500|502|503|overloaded|server_error|api_error|service.?unavailable|context (?:window|length) exceed|context window exceed/i;
+// Provider adapters throw this when an upstream stop reason reaches Pi before
+// the adapter knows how to map it. Keep the match scoped so plain "unknown"
+// runtime errors still pause for inspection instead of being retried forever.
+const PROVIDER_STOP_REASON_RE = /unhandled stop reason:\s*(?:abort|unknown)\b/i;
 // ECONNRESET/ECONNREFUSED are in NETWORK_RE (same-model retry first).
-const CONNECTION_RE = /terminated|connection.?(?:refused|error)|other side closed|EPIPE|network.?(?:is\s+)?unavailable|stream_exhausted(?:_without_result)?/i;
+const CONNECTION_RE = /terminated|\babort\b|connection.?(?:refused|error)|other side closed|EPIPE|network.?(?:is\s+)?unavailable|stream_exhausted(?:_without_result)?/i;
 // Catch-all for V8 JSON.parse errors: all modern variants end with "in JSON at position \d+".
 // This eliminates the need to enumerate every error message variant individually.
 const STREAM_RE = /in JSON at position \d+|Unexpected end of JSON|SyntaxError.*JSON/i;
@@ -72,7 +76,7 @@ const UNSUPPORTED_MODEL_SCOPE_RE = /\b(?:account|plan|tier|subscription)\b/i;
  *  3. Network (ECONNRESET, ETIMEDOUT, socket hang up, fetch failed, dns)
  *  4. Stream truncation (malformed JSON from mid-stream cut)
  *  5. Server (500/502/503, overloaded, server_error)
- *  6. Connection (terminated, ECONNREFUSED, EPIPE, other side closed)
+ *  6. Connection (terminated, abort/unknown stop reason, ECONNREFUSED, EPIPE, other side closed)
  *  7. Model error (400 invalid argument / payload rejected for this model)
  *  8. Unknown
  */
@@ -124,6 +128,12 @@ export function classifyError(errorMsg, retryAfterMs) {
         const delayMs = resetMatch ? Number(resetMatch[1]) * 1000 : 60_000;
         return { kind: "rate-limit", retryAfterMs: delayMs };
     }
+    // Provider stop-reason adapter gaps are usually request/stream failures from
+    // the current model. Treat the scoped adapter message as fallback-eligible,
+    // but keep generic unknown errors on the indefinite pause path.
+    if (PROVIDER_STOP_REASON_RE.test(errorMsg)) {
+        return { kind: "connection", retryAfterMs: retryAfterMs ?? 15_000 };
+    }
     // 3. Network errors — same-model retry candidate
     if (NETWORK_RE.test(errorMsg)) {
         // Exclude if also matches permanent signals (already handled above for

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

@@ -33,6 +33,7 @@ export const EXEC_DEFAULTS = {
         "LOGNAME",
         "TMPDIR",
         "NODE_OPTIONS",
+        "NODE_PATH",
         "PYTHONPATH",
         "PYTHONIOENCODING",
     ],