@lsctech/polaris 0.5.12 → 0.5.14

package/dist/cli/adopt-canon.js

@@ -6,6 +6,7 @@ const node_path_1 = require("node:path");
 const node_child_process_1 = require("node:child_process");
 const loader_js_1 = require("../config/loader.js");
 const librarian_dispatch_js_1 = require("../smartdocs-engine/librarian-dispatch.js");
+const seed_instructions_js_1 = require("../smartdocs-engine/seed-instructions.js");
 const SKIP_DIRS = new Set(["node_modules", ".git", "dist", "build", ".polaris", "smartdocs"]);
 function loadInventoryCanonicalFolders(repoRoot) {
     const inventoryPath = (0, node_path_1.join)(repoRoot, ".polaris", "adoption-inventory.json");
@@ -29,7 +30,7 @@ function scaffoldDraftSummaryFiles(repoRoot, canonicalFolders) {
         if ((0, node_fs_1.existsSync)(summaryPath))
             continue;
         (0, node_fs_1.mkdirSync)(dir, { recursive: true });
-        (0, node_fs_1.writeFileSync)(summaryPath, `# ${folder}\n\n<!-- polaris:draft -->\n`, "utf-8");
+        (0, node_fs_1.writeFileSync)(summaryPath, (0, seed_instructions_js_1.generateSummaryDraft)(folder, repoRoot, {}), "utf-8");
         console.log(`  Scaffolded draft SUMMARY.md: ${folder}`);
     }
 }
@@ -90,13 +91,19 @@ function injectLinkedDocs(content, docs, summaryLines) {
     const headingIdx = lines.findIndex((l) => l.startsWith("#"));
     if (headingIdx === -1)
         return content;
+    const heading = lines[headingIdx];
+    const hasSummaryContent = summaryLines.length > 0;
     const yamlLines = ["", "---", ...buildLinkedDocsBlock(docs), "---"];
-    const before = lines.slice(0, headingIdx + 1);
-    // If agent provided summary content, append after YAML block
-    const after = summaryLines.length > 0
-        ? ["", ...summaryLines]
-        : lines.slice(headingIdx + 1);
-    return [...before, ...yamlLines, ...after].join("\n");
+    const bodyLines = hasSummaryContent
+        ? [...yamlLines, "", ...summaryLines]
+        : [...yamlLines, ...lines.slice(headingIdx + 1).filter((l) => {
+                const t = l.trim();
+                return t !== seed_instructions_js_1.DRAFT_MARKER && t !== seed_instructions_js_1.GENERATED_START_MARKER && t !== seed_instructions_js_1.GENERATED_END_MARKER;
+            })];
+    const generatedRegion = [heading, ...bodyLines].join("\n");
+    return hasSummaryContent
+        ? [seed_instructions_js_1.GENERATED_START_MARKER, generatedRegion, seed_instructions_js_1.GENERATED_END_MARKER].join("\n")
+        : [seed_instructions_js_1.DRAFT_MARKER, seed_instructions_js_1.GENERATED_START_MARKER, generatedRegion, seed_instructions_js_1.GENERATED_END_MARKER].join("\n");
 }
 function parseCanonResponse(text) {
     const trimmed = text.trim();
@@ -249,12 +256,19 @@ async function enrichCanonFiles(repoRoot) {
         if ((response.polaris_lines ?? []).length > 0) {
             const polarisPath = (0, node_path_1.join)(dir, "POLARIS.md");
             const polarisContent = [
+                seed_instructions_js_1.GENERATED_START_MARKER,
                 `# POLARIS — ${routeFolder}`,
                 "",
                 ...response.polaris_lines,
                 "",
+                seed_instructions_js_1.GENERATED_END_MARKER,
             ].join("\n");
-            (0, node_fs_1.writeFileSync)(polarisPath, polarisContent, "utf-8");
+            if (!(0, node_fs_1.existsSync)(polarisPath) || (0, seed_instructions_js_1.hasDraftMarker)(polarisPath)) {
+                (0, node_fs_1.writeFileSync)(polarisPath, polarisContent, "utf-8");
+            }
+            else {
+                console.log(`  Skipping POLARIS.md (existing non-draft): ${routeFolder}`);
+            }
         }
         enrichedCount++;
         console.log(`  ✓ Enriched ${routeFolder} with ${response.relevant_docs.length} linked docs`);

package/dist/finalize/artifact-policy.js

@@ -24,23 +24,6 @@ const LEGACY_RUN_ARTIFACTS = new Set([
     ".polaris/runs/run-report.md",
     ".polaris/runs/current-state.pre-pol-198.json",
 ]);
-function isPromotedRunArchivePath(relativePath) {
-    if (!relativePath.startsWith(".polaris/runs/")) {
-        return false;
-    }
-    const rest = relativePath.slice(".polaris/runs/".length);
-    if (rest === "" || rest === "evo-run-archive") {
-        return false;
-    }
-    const slashIndex = rest.indexOf("/");
-    if (slashIndex === -1) {
-        // The path is a directory-style run archive path (e.g. `.polaris/runs/<run-id>`),
-        // not a top-level file like `ledger.jsonl`.
-        return !rest.includes(".") && !rest.startsWith(".");
-    }
-    const firstSegment = rest.slice(0, slashIndex);
-    return firstSegment !== "evo-run-archive";
-}
 function normalizeArtifactPath(filePath) {
     const normalized = node_path_1.default.posix.normalize(filePath.replace(/\\/g, "/"));
     return normalized.startsWith("./") ? normalized.slice(2) : normalized;
@@ -78,9 +61,6 @@ function classifyArtifactPath(filePath, activeClusterId) {
     if (relativePath === PROMOTED_RUN_LEDGER) {
         return "promoted-run-ledger";
     }
-    if (isPromotedRunArchivePath(relativePath)) {
-        return "promoted-run-archive";
-    }
     if (relativePath.startsWith(PROMOTED_COGNITION_ARCHIVE_PREFIX)) {
         return "promoted-cognition-archive";
     }
@@ -102,7 +82,6 @@ function isPromotedArtifactPath(filePath, activeClusterId) {
     const classification = classifyArtifactPath(filePath, activeClusterId);
     return (classification === "promoted-cluster-artifact"
         || classification === "promoted-run-ledger"
-        || classification === "promoted-run-archive"
         || classification === "promoted-cognition-archive"
         || classification === "promoted-map-artifact");
 }
@@ -114,8 +93,6 @@ function explainArtifactPolicy(filePath, activeClusterId) {
             return "active cluster evidence is eligible for promotion into finalize commits";
         case "promoted-run-ledger":
             return "the run ledger is durable audit evidence and stays commit-eligible";
-        case "promoted-run-archive":
-            return "archived run snapshots under .polaris/runs/<run-id>/ are durable audit evidence and stay commit-eligible";
         case "promoted-cognition-archive":
             return "archived cognition reconciliation notes are durable provenance and stay commit-eligible";
         case "promoted-map-artifact":
@@ -139,7 +116,6 @@ function findArtifactPromotionViolations(stagedPaths, activeClusterId) {
         if (classification === "non-artifact"
             || classification === "promoted-cluster-artifact"
             || classification === "promoted-run-ledger"
-            || classification === "promoted-run-archive"
             || classification === "promoted-cognition-archive"
             || classification === "promoted-map-artifact") {
             continue;
@@ -194,6 +170,7 @@ function getGitignorePatterns() {
         ".polaris/runs/current-state.json",
         ".polaris/runs/run-report.md",
         ".polaris/runs/current-state.pre-pol-198.json",
+        ".polaris/runs/*/",
         ".polaris/runs/evo-run-archive/**",
         ".polaris/bootstrap/**",
         ".polaris/session-type",

package/dist/finalize/index.js

@@ -246,7 +246,7 @@ function checkLibrarianGate(repoRoot, clusterId) {
 }
 function resolveQcTelemetryFile(state, repoRoot) {
     const artifactDir = state.artifact_dir ?? (0, node_path_1.join)(repoRoot, ".taskchain_artifacts", "polaris-run");
-    return (0, node_path_1.join)(artifactDir, "runs", state.run_id, "telemetry.jsonl");
+    return (0, node_path_1.resolve)(repoRoot, artifactDir, "runs", state.run_id, "telemetry.jsonl");
 }
 // ── QC repair-loop terminal state gate ────────────────────────────────────────
 /**
@@ -628,7 +628,7 @@ async function runFinalize(options) {
             throw new Error(`Canon check cannot proceed: git diff failed: ${msg}`);
         }
         const artifactDirForCheck = state.artifact_dir ?? (0, node_path_1.join)(repoRoot, ".taskchain_artifacts", "polaris-run");
-        const telemetryFileForCheck = (0, node_path_1.join)(artifactDirForCheck, "runs", state.run_id, "telemetry.jsonl");
+        const telemetryFileForCheck = (0, node_path_1.resolve)(repoRoot, artifactDirForCheck, "runs", state.run_id, "telemetry.jsonl");
         const canonResult = (0, canon_check_js_1.runCanonCheck)({
             repoRoot,
             changedFiles,
@@ -867,6 +867,13 @@ async function runFinalize(options) {
     console.log("[8/14] Committing durable Polaris state + map..."); // Step count updated
     const resolvedStateFile = (0, node_path_1.resolve)(stateFile);
     (0, _06_commit_js_1.stepCommit)(repoRoot, state, resolvedStateFile, reportPath);
+    // The run's local state file is the authoritative place for post-PR state
+    // (pr_url, status: complete). When the state file passed to finalize is the
+    // tracked cluster snapshot, redirect post-PR writes to the untracked per-run
+    // archive so the cluster snapshot is never written after PR creation.
+    const runLocalStateFile = isClusterStateSnapshotFile(resolvedStateFile)
+        ? (0, node_path_1.resolve)(repoRoot, ".polaris", "runs", state.run_id, "current-state.json")
+        : resolvedStateFile;
     if (skipDelivery) {
         console.log("[9–14/14] Delivery skipped (--skip-delivery).");
         console.log("polaris finalize steps 1–8 complete.");
@@ -890,24 +897,13 @@ async function runFinalize(options) {
         prUrl,
         stepLabel: "[10.5/14]",
     });
-    // Step 11: Write PR URL to current-state.json
+    // Step 11: Write PR URL to the run's local state file
     console.log("[11/14] Writing PR URL to state...");
-    state = (0, _09_update_state_js_1.stepUpdateState)(resolvedStateFile, state, prUrl);
-    // Promote the authoritative run state into the cluster snapshot so that
-    // `.polaris/clusters/<id>/state.json` preserves completed children, the
-    // dispatch boundary, QC repair-loop terminal state, and the PR URL.
-    try {
-        const clusterStateSnapshotPath = (0, node_path_1.join)(repoRoot, ".polaris", "clusters", state.cluster_id, "state.json");
-        (0, checkpoint_js_1.writeStateAtomic)(clusterStateSnapshotPath, state);
-    }
-    catch (snapshotError) {
-        process.stderr.write(`[11/14] WARNING: Failed to write cluster state snapshot: ${snapshotError instanceof Error ? snapshotError.message : String(snapshotError)}\n`);
-        process.stderr.write(`Delivery will proceed, but cluster state snapshot at .polaris/clusters/${state.cluster_id}/state.json may be incomplete.\n`);
-    }
+    state = (0, _09_update_state_js_1.stepUpdateState)(runLocalStateFile, state, prUrl);
     // Step 12: Append JSONL events
     console.log("[12/14] Appending JSONL events...");
     const artifactDir = state.artifact_dir ?? (0, node_path_1.join)(repoRoot, ".taskchain_artifacts", "polaris-run");
-    const telemetryFile = (0, node_path_1.join)(artifactDir, "runs", state.run_id, "telemetry.jsonl");
+    const telemetryFile = (0, node_path_1.resolve)(repoRoot, artifactDir, "runs", state.run_id, "telemetry.jsonl");
     (0, _10_append_jsonl_js_1.stepAppendJsonl)(telemetryFile, state, prUrl);
     // Step 13: Update Linear parent issue
     console.log("[13/14] Updating Linear...");
@@ -916,7 +912,7 @@ async function runFinalize(options) {
     await (0, _11_update_linear_js_1.stepUpdateLinear)(state, branch, prUrl, true, linearEnabled, state.cluster_id, lifecyclePolicy, authChildResult.authoritativeCount);
     // Step 14: Archive run snapshot
     console.log("[14/14] Archiving run snapshot...");
-    (0, _12_archive_js_1.stepArchive)(repoRoot, state, resolvedStateFile, reportPath);
+    (0, _12_archive_js_1.stepArchive)(repoRoot, state, runLocalStateFile, reportPath);
     console.log("polaris finalize complete.");
 }
 function failMissingSubcommand(command, commandName) {

package/dist/finalize/run-report.js

@@ -155,9 +155,9 @@ function renderRoutingSection(state, telemetryEvents) {
         : "No routing anomalies or evidence gaps detected.";
     return `### Provider distribution
 
-| Child | Provider | Selection reason | Mode | Policy order | Candidates | Fallbacks | Status |
-|---|---|---|---|---|---|---|---|
-${rows || "| _No children recorded_ | — | — | — | — | — | — | — |"}
+| Child | Title | Provider | Selection reason | Mode | Policy order | Candidates | Fallbacks | Status |
+|---|---|---|---|---|---|---|---|---|
+${rows || "| _No children recorded_ | — | — | — | — | — | — | — | — |"}
 
 **Provider summary:** ${distribution}
 

package/dist/finalize/steps/06-commit.js

@@ -7,8 +7,7 @@ const node_path_1 = require("node:path");
 const artifact_policy_js_1 = require("../artifact-policy.js");
 function stepCommit(repoRoot, state, _stateFile, _reportPath) {
     const msg = `polaris finalize: ${state.run_id}\n\nChildren: ${state.completed_children.length} completed\nBranch: ${getBranch(repoRoot)}`;
-    const runArchiveTarget = `.polaris/runs/${state.run_id}`;
-    const promotedTargets = [...(0, artifact_policy_js_1.getArtifactPromotionStageTargets)(state.cluster_id), runArchiveTarget]
+    const promotedTargets = (0, artifact_policy_js_1.getArtifactPromotionStageTargets)(state.cluster_id)
         .filter((target) => (0, node_fs_1.existsSync)((0, node_path_1.join)(repoRoot, target)));
     if (promotedTargets.length > 0) {
         (0, node_child_process_1.execFileSync)("git", ["add", "--", ...promotedTargets], { cwd: repoRoot, stdio: "inherit" });

package/dist/finalize/steps/12-archive.js

@@ -19,7 +19,7 @@ function stepArchive(repoRoot, state, stateFile, reportPath) {
     }
     const artifactDir = state.artifact_dir
         ?? (0, node_path_1.join)(repoRoot, ".taskchain_artifacts", "polaris-run");
-    const telemetryFile = (0, node_path_1.join)(artifactDir, "runs", state.run_id, "telemetry.jsonl");
+    const telemetryFile = (0, node_path_1.resolve)(repoRoot, artifactDir, "runs", state.run_id, "telemetry.jsonl");
     if ((0, node_fs_1.existsSync)(telemetryFile)) {
         (0, node_fs_1.copyFileSync)(telemetryFile, (0, node_path_1.join)(archiveDir, "telemetry.jsonl"));
     }

package/dist/loop/adapters/cli-subtask-bridge.js

@@ -61,10 +61,12 @@ function writeSealedResultFromSummary(packet, parsedSummary) {
     }
     const commit = (typeof parsedSummary["commit"] === "string" && parsedSummary["commit"]) ||
         (typeof parsedSummary["commit_hash"] === "string" && parsedSummary["commit_hash"]) ||
+        (typeof parsedSummary["commit_sha"] === "string" && parsedSummary["commit_sha"]) ||
         undefined;
     const validation = parsedSummary["validation"] ?? parsedSummary["validation_summary"];
     const sealedResult = {
         run_id: packet.run_id,
+        cluster_id: packet.cluster_id,
         child_id: packet.active_child,
         status: normalizeSealedStatus(parsedSummary["status"]),
     };

package/dist/loop/adapters/terminal-cli.js

@@ -498,15 +498,42 @@ class TerminalCliAdapter {
             const compact = buildCompactReturnForSealedResult(normalized, exitCode);
             const compactReturnErrors = (0, compact_return_js_1.validateCompactReturn)(compact);
             const isValidCompactReturn = compactReturnErrors.length === 0;
-            const finalStatus = isValidCompactReturn
+            let finalStatus = isValidCompactReturn
                 ? compact["status"]
                 : "failed";
-            const finalValidation = isValidCompactReturn
+            let finalValidation = isValidCompactReturn
                 ? compact["validation"]
                 : "failed";
-            const finalNext = isValidCompactReturn
+            let finalNext = isValidCompactReturn
                 ? compact["next_recommended_action"]
                 : "stop";
+            // Reconcile validation/next_recommended_action with run-health symptoms.
+            // A validation-failed symptom overrides a passing validation string and
+            // prevents a continue recommendation when the build/tests did not pass.
+            const rawSymptoms = compact["run_health_symptoms"];
+            const hasValidationFailedSymptom = Array.isArray(rawSymptoms) &&
+                rawSymptoms.some((s) => typeof s === "object" &&
+                    s !== null &&
+                    s["category"] === "validation-failed");
+            if (hasValidationFailedSymptom) {
+                finalValidation = "failed";
+                finalNext = "stop";
+            }
+            // "continue" requires a passing validation result. If validation failed,
+            // the recommendation must be a terminal stop. If validation was skipped,
+            // treat the successful exit as a pass for the completion contract.
+            if (finalStatus === "done" && finalNext === "continue") {
+                if (finalValidation === "failed") {
+                    finalNext = "stop";
+                }
+                else if (finalValidation === "skipped") {
+                    finalValidation = "passed";
+                }
+            }
+            // A failed status should never recommend continuation.
+            if ((finalStatus === "failed" || finalStatus === "blocked") && finalNext === "continue") {
+                finalNext = "stop";
+            }
             const errorMessage = finalStatus === "failed" || finalStatus === "blocked"
                 ? isValidCompactReturn
                     ? typeof compact["error_message"] === "string"
@@ -518,6 +545,7 @@ class TerminalCliAdapter {
                 : undefined;
             const sealedResult = {
                 run_id: packet.run_id,
+                cluster_id: packet.cluster_id,
                 child_id: compact["child_id"],
                 status: finalStatus,
                 commit: compact["commit"],

package/dist/loop/body-parser.js

@@ -168,6 +168,10 @@ function normalizeDirectoryPattern(pattern) {
     // Extract the final path segment to check for extensions
     const lastSlashIndex = pattern.lastIndexOf('/');
     const finalSegment = lastSlashIndex >= 0 ? pattern.slice(lastSlashIndex + 1) : pattern;
+    // Dot-files that are files, not directories, must not get a trailing `/**`.
+    if (finalSegment === '.gitignore' || finalSegment === '.gitattributes') {
+        return pattern;
+    }
     // Check if final segment has a file extension (not counting leading dot in dot-directories)
     const hasExtension = finalSegment.startsWith('.')
         ? finalSegment.slice(1).includes('.') // For .github, .vscode: no extension. For .env.local: has extension

package/dist/loop/continue.js

@@ -215,7 +215,7 @@ function appendTelemetryEvent(telemetryFile, event) {
 }
 function resolveTelemetryFilePath(state, repoRoot) {
     const artifactDir = state.artifact_dir ?? (0, node_path_1.join)(repoRoot, ".taskchain_artifacts", "polaris-run");
-    return (0, node_path_1.join)(artifactDir, "runs", state.run_id, "telemetry.jsonl");
+    return (0, node_path_1.resolve)(repoRoot, artifactDir, "runs", state.run_id, "telemetry.jsonl");
 }
 function hasValidationEvidence(validation) {
     if (validation === undefined || validation === null)
@@ -383,7 +383,7 @@ function runLoopContinue(options) {
     // If no dispatch was recorded (dispatch_epoch === continue_epoch),
     // reject immediately and do NOT mutate any state.
     const artifactDirForTelemetry = state.artifact_dir ?? (0, node_path_1.join)(repoRoot, ".taskchain_artifacts", "polaris-run");
-    const telemetryFileForCheck = (0, node_path_1.join)(artifactDirForTelemetry, "runs", state.run_id, "telemetry.jsonl");
+    const telemetryFileForCheck = (0, node_path_1.resolve)(repoRoot, artifactDirForTelemetry, "runs", state.run_id, "telemetry.jsonl");
     try {
         (0, dispatch_boundary_js_1.assertContinueRequiresDispatch)(state, telemetryFileForCheck);
     }
@@ -622,7 +622,7 @@ function runLoopContinue(options) {
     appendContinueLedgerEvents(repoRoot, updatedState, completedChild);
     // Step 2: Append JSONL checkpoint event
     const artifactDir = state.artifact_dir ?? (0, node_path_1.join)(repoRoot, ".taskchain_artifacts", "polaris-run");
-    const telemetryFile = (0, node_path_1.join)(artifactDir, "runs", state.run_id, "telemetry.jsonl");
+    const telemetryFile = (0, node_path_1.resolve)(repoRoot, artifactDir, "runs", state.run_id, "telemetry.jsonl");
     (0, checkpoint_js_1.appendCheckpointEvent)(telemetryFile, {
         event: "loop-checkpoint",
         run_id: state.run_id,

package/dist/loop/dispatch.js

@@ -373,7 +373,7 @@ function appendTelemetry(telemetryFile, event) {
 }
 function resolveTelemetryFile(state, repoRoot) {
     const artifactDir = state.artifact_dir ?? (0, node_path_1.join)(repoRoot, ".taskchain_artifacts", "polaris-run");
-    return (0, node_path_1.join)(artifactDir, "runs", state.run_id, "telemetry.jsonl");
+    return (0, node_path_1.resolve)(repoRoot, artifactDir, "runs", state.run_id, "telemetry.jsonl");
 }
 function canonicalPath(path) {
     try {

package/dist/loop/orphan-recovery.js

@@ -177,12 +177,13 @@ function resetForRedispatch(stateFile, state, childId) {
     if (!childMeta?.dispatch_record)
         return (0, node_crypto_1.randomUUID)();
     const newDispatchId = (0, node_crypto_1.randomUUID)();
-    // Clear dispatch record but retain audit trail via telemetry
+    // Clear dispatch record and result_file to prevent stale artifact reads
     const updatedMeta = {
         ...state.open_children_meta,
         [childId]: {
             ...childMeta,
             dispatch_record: undefined,
+            result_file: undefined,
         },
     };
     // Reset active_child so a new dispatch can proceed

package/dist/loop/parent.js

@@ -120,7 +120,7 @@ function appendTelemetry(telemetryFile, event) {
 }
 function resolveTelemetryFile(state, repoRoot) {
     const artifactDir = state.artifact_dir ?? (0, node_path_1.join)(repoRoot, ".taskchain_artifacts", "polaris-run");
-    return (0, node_path_1.join)(artifactDir, "runs", state.run_id, "telemetry.jsonl");
+    return (0, node_path_1.resolve)(repoRoot, artifactDir, "runs", state.run_id, "telemetry.jsonl");
 }
 function estimateTokensFromBytes(bytes) {
     return Math.round(bytes / 4);
@@ -685,6 +685,23 @@ async function runParentLoop(options) {
     if (!dryRun) {
         appendRunStartedLedgerEvent(repoRoot, state);
     }
+    // Keep the canonical cluster snapshot in sync with the taskchain state so
+    // `polaris status`, `polaris continue`, and `polaris finalize` always see
+    // the freshest state, even if the parent loop is interrupted before it
+    // reaches the final cluster-complete write.
+    const canonicalStatePath = (0, node_path_1.join)(repoRoot, ".polaris", "clusters", state.cluster_id, "state.json");
+    const writeStateAtomic = (filePath, stateToWrite) => {
+        (0, checkpoint_js_1.writeStateAtomic)(filePath, stateToWrite);
+        if ((0, node_path_1.resolve)(filePath) !== (0, node_path_1.resolve)(canonicalStatePath)) {
+            try {
+                (0, checkpoint_js_1.writeStateAtomic)(canonicalStatePath, stateToWrite);
+            }
+            catch (err) {
+                const msg = err instanceof Error ? err.message : String(err);
+                process.stderr.write(`[polaris] canonical cluster state snapshot at ${canonicalStatePath} failed to update and remains stale: ${msg}\n`);
+            }
+        }
+    };
     // Load config for adapter and provider resolution
     const config = (0, loader_js_1.loadConfig)(repoRoot);
     const legacyOrchestrationMode = state["orchestration_mode"];
@@ -1053,11 +1070,11 @@ async function runParentLoop(options) {
                             onStateUpdate: (loopState) => {
                                 // Persist loop state to the state file on each mutation.
                                 const stateWithLoop = { ...state, qc_repair_loop: loopState };
-                                (0, checkpoint_js_1.writeStateAtomic)(stateFile, stateWithLoop);
+                                writeStateAtomic(stateFile, stateWithLoop);
                             },
                         });
                         state = { ...state, qc_repair_loop: repairLoopResult.loop_state };
-                        (0, checkpoint_js_1.writeStateAtomic)(stateFile, state);
+                        writeStateAtomic(stateFile, state);
                         appendTelemetry(telemetryFile, {
                             event: "qc-repair-loop-finished",
                             run_id: state.run_id,
@@ -1179,8 +1196,7 @@ async function runParentLoop(options) {
             if (!dryRun) {
                 logStatus(notificationFormat, "COMPLETE");
                 const clusterCompleteState = { ...state, status: "cluster-complete" };
-                (0, checkpoint_js_1.writeStateAtomic)(stateFile, clusterCompleteState);
-                (0, checkpoint_js_1.writeStateAtomic)((0, node_path_1.join)(repoRoot, '.polaris', 'clusters', state.cluster_id, 'state.json'), clusterCompleteState);
+                writeStateAtomic(stateFile, clusterCompleteState);
                 appendTelemetry(telemetryFile, {
                     event: "cluster-complete",
                     run_id: state.run_id,
@@ -1240,7 +1256,7 @@ async function runParentLoop(options) {
         if (budgetCheck.status === 'exhausted') {
             // Write checkpoint before halting
             if (!dryRun) {
-                (0, checkpoint_js_1.writeStateAtomic)(stateFile, {
+                writeStateAtomic(stateFile, {
                     ...state,
                     status: "budget-exhausted",
                     step_cursor: "budget-check",
@@ -1514,7 +1530,7 @@ async function runParentLoop(options) {
                 step_cursor: "dispatch",
                 dispatch_boundary: (0, dispatch_boundary_js_1.advanceDispatchEpoch)(state.dispatch_boundary, nextChild),
             };
-            (0, checkpoint_js_1.writeStateAtomic)(stateFile, stateWithDispatch);
+            writeStateAtomic(stateFile, stateWithDispatch);
             state = stateWithDispatch;
             stateBeforeDispatch = stateWithDispatch;
             try {
@@ -1617,7 +1633,7 @@ async function runParentLoop(options) {
         // No result file was written. Roll back dispatch state so the run is
         // cleanly resumable without manual `loop abort` intervention.
         if (dispatchResult.pre_dispatch_failure && !dryRun) {
-            (0, checkpoint_js_1.writeStateAtomic)(stateFile, statePreDispatch);
+            writeStateAtomic(stateFile, statePreDispatch);
             appendTelemetry(telemetryFile, {
                 event: "pre-dispatch-failure",
                 run_id: state.run_id,
@@ -1768,7 +1784,7 @@ async function runParentLoop(options) {
                     timestamp: new Date().toISOString(),
                 });
                 // Write checkpoint with blocker information
-                (0, checkpoint_js_1.writeStateAtomic)(stateFile, {
+                writeStateAtomic(stateFile, {
                     ...state,
                     status: "blocked",
                     step_cursor: "blocked",
@@ -2153,7 +2169,7 @@ async function runParentLoop(options) {
             childrenDispatched += 1;
             // Worker did not write its own completion — orchestrator fills the gap.
             if (!dryRun) {
-                (0, checkpoint_js_1.writeStateAtomic)(stateFile, state);
+                writeStateAtomic(stateFile, state);
             }
         }
         else {
@@ -2169,7 +2185,7 @@ async function runParentLoop(options) {
             }, nextChild);
             childrenDispatched += 1;
             if (!dryRun) {
-                (0, checkpoint_js_1.writeStateAtomic)(stateFile, state);
+                writeStateAtomic(stateFile, state);
             }
         }
         // Orchestrator checkpoint event — always emitted after a successful child.
@@ -2269,7 +2285,7 @@ async function runParentLoop(options) {
             if (postBudgetCheck.status === 'exhausted') {
                 const nextPending = state.open_children[0] ?? null;
                 if (!dryRun) {
-                    (0, checkpoint_js_1.writeStateAtomic)(stateFile, {
+                    writeStateAtomic(stateFile, {
                         ...state,
                         status: "budget-exhausted",
                         step_cursor: "budget-check",

package/dist/loop/run-bootstrap.js

@@ -141,6 +141,8 @@ function runLoopBootstrapInit(options) {
     const runId = options.runId ?? deriveRunId(clusterId);
     const seal = createBootstrapSeal(runId, clusterId, openChildren);
     const deliveryBranch = branch ?? (0, git_custody_js_1.buildDeliveryBranchName)(clusterId);
+    const resolvedArtifactDir = (0, node_path_1.resolve)(repoRoot, artifactDir ?? (0, node_path_1.join)(repoRoot, ".taskchain_artifacts", "polaris-run"));
+    const artifactDirValue = (0, node_path_1.relative)(repoRoot, resolvedArtifactDir);
     const initialState = {
         schema_version: "1.0",
         run_id: runId,
@@ -159,7 +161,7 @@ function runLoopBootstrapInit(options) {
         },
         status: "running",
         next_open_child: openChildren[0] ?? null,
-        artifact_dir: artifactDir ?? (0, node_path_1.join)(repoRoot, ".taskchain_artifacts", "polaris-run"),
+        artifact_dir: artifactDirValue,
         dispatch_boundary: (0, dispatch_boundary_js_2.initialDispatchBoundary)(),
         run_bootstrap_seal: seal,
     };

package/dist/map/inference.js

@@ -17,7 +17,10 @@ function inferRoute(filePath, repoRoot, config, knownRoutes, branchName) {
             const subdir = rest.split("/")[0];
             if (subdir && rest.includes("/")) {
                 domain = subdir;
-                route = `${sourceRoot}/${subdir}`;
+                // Route identity follows the file's own containing directory, not just the
+                // top-level domain subdir — otherwise nested folders (e.g. src/runtime/continuation)
+                // incorrectly report the parent domain's route (e.g. src/runtime).
+                route = (0, node_path_1.dirname)(filePath).replace(/\\/g, "/");
                 taskchain = `polaris-${subdir}`;
                 confidence += 0.85;
                 tags.push(subdir);

package/dist/medic/run-health-consult.js

@@ -114,11 +114,12 @@ function markInProgress(report, chartRef, repoRoot) {
     (0, index_js_1.markMedicDecision)(report.run_id, { status: "in-progress", chartRefs: [chartRef] }, repoRoot);
 }
 function markResolved(report, chartRef, treatmentRefs, outcome, repoRoot) {
+    const success = outcome === "treatment-success" || outcome === "no-treatment-needed";
     (0, index_js_1.markMedicDecision)(report.run_id, {
-        status: "resolved",
+        status: success ? "resolved" : "in-progress",
         chartRefs: [chartRef],
         treatmentPacketRefs: treatmentRefs,
-        resolvedAt: new Date().toISOString(),
+        resolvedAt: success ? new Date().toISOString() : undefined,
         resolutionNotes: `Terminal outcome: ${outcome}`,
     }, repoRoot);
 }
@@ -355,7 +356,7 @@ async function runMedicRunHealthConsult(input) {
                 run_id: packet.run_id,
                 cluster_id: packet.cluster_id,
                 dispatch_id: packet.dispatch_id,
-                status: "resolved",
+                status: "blocked",
                 chart_id: chart.chart_id,
                 decision: "terminal",
                 treatment_packet_refs: allTreatmentRefs,
@@ -371,7 +372,7 @@ async function runMedicRunHealthConsult(input) {
         run_id: packet.run_id,
         cluster_id: packet.cluster_id,
         dispatch_id: packet.dispatch_id,
-        status: "resolved",
+        status: remainingSymptoms.length === 0 ? "resolved" : "blocked",
         chart_id: chart.chart_id,
         decision: "terminal",
         treatment_packet_refs: allTreatmentRefs,

package/dist/medic/treatment-packets.js

@@ -59,7 +59,7 @@ function buildTreatmentPackets(input) {
     return treated.map((symptom) => {
         const packetId = buildTreatmentPacketId(report.run_id, round, symptom.id);
         const dispatchId = (0, node_crypto_1.randomUUID)();
-        const resultFile = (0, node_path_1.join)(getMedicDir(report.cluster_id, repoRoot), `${packetId}-result.json`);
+        const resultFile = (0, node_path_1.relative)(repoRoot, (0, node_path_1.join)(getMedicDir(report.cluster_id, repoRoot), `${packetId}-result.json`));
         return {
             packet_id: packetId,
             run_id: report.run_id,
@@ -154,12 +154,16 @@ async function dispatchTreatmentWorker(input) {
     const result = await dispatch(workerPacket);
     const summary = parseTreatmentWorkerSummary(result.summary);
     if (result.exit_code === 0 && summary?.status === "done") {
+        const completedTreatment = { ...treatment, status: "completed" };
+        writeTreatmentPacket({ treatment: completedTreatment, repoRoot });
         return {
             packet_id: treatment.packet_id,
             status: "success",
             commit_sha: summary.commit,
         };
     }
+    const failedTreatment = { ...treatment, status: "failed" };
+    writeTreatmentPacket({ treatment: failedTreatment, repoRoot });
     return {
         packet_id: treatment.packet_id,
         status: "failure",

package/dist/qc/providers/coderabbit.js

@@ -148,6 +148,8 @@ function isErrorRecord(record) {
         return true;
     if (record.error === true || record.error === "true")
         return true;
+    if (typeof record.status === "string" && record.status.toLowerCase() === "error")
+        return true;
     return false;
 }
 function errorTypeFromRecord(record) {

package/dist/run-health/index.js

@@ -150,6 +150,18 @@ function appendSymptom(runId, symptom, repoRoot) {
         symptoms: [...existing.symptoms, symptom],
         updated_at: new Date().toISOString(),
     };
+    // A later high/critical symptom means a previously resolved Medic consult is
+    // no longer satisfied; reopen it so closeout/medic gates do not pass on a
+    // stale resolved decision.
+    if (existing.medic_consult?.status === "resolved" &&
+        (symptom.severity === "critical" || symptom.severity === "high")) {
+        updated.medic_consult = {
+            ...existing.medic_consult,
+            status: "in-progress",
+            resolved_at: undefined,
+            resolution_notes: undefined,
+        };
+    }
     const validation = (0, schema_js_1.validateRunHealthReport)(updated);
     if (!validation.valid) {
         throw new Error(`Appended symptom produces invalid report:\n${validation.errors.join("\n")}`);