gsd-pi 2.37.1-dev.d3ace49 → 2.38.0-dev.29edcdc

package/src/resources/extensions/gsd/auto-post-unit.ts

@@ -33,7 +33,6 @@ import { writeUnitRuntimeRecord, clearUnitRuntimeRecord } from "./unit-runtime.j
 import { runGSDDoctor, rebuildState, summarizeDoctorIssues } from "./doctor.js";
 import { recordHealthSnapshot, checkHealEscalation } from "./doctor-proactive.js";
 import { syncStateToProjectRoot } from "./auto-worktree-sync.js";
-import { resetRewriteCircuitBreaker } from "./auto-dispatch.js";
 import { isDbAvailable } from "./gsd-db.js";
 import { consumeSignal } from "./session-status-io.js";
 import {
@@ -56,6 +55,13 @@ import { join } from "node:path";
 /** Throttle STATE.md rebuilds — at most once per 30 seconds */
 const STATE_REBUILD_MIN_INTERVAL_MS = 30_000;
 
+export interface PreVerificationOpts {
+  skipSettleDelay?: boolean;
+  skipDoctor?: boolean;
+  skipStateRebuild?: boolean;
+  skipWorktreeSync?: boolean;
+}
+
 export interface PostUnitContext {
   s: AutoSession;
   ctx: ExtensionContext;
@@ -73,7 +79,7 @@ export interface PostUnitContext {
  *
  * Returns "dispatched" if a signal caused stop/pause, "continue" to proceed.
  */
-export async function postUnitPreVerification(pctx: PostUnitContext): Promise<"dispatched" | "continue"> {
+export async function postUnitPreVerification(pctx: PostUnitContext, opts?: PreVerificationOpts): Promise<"dispatched" | "continue"> {
   const { s, ctx, pi, buildSnapshotOpts, stopAuto, pauseAuto } = pctx;
 
   // ── Parallel worker signal check ──
@@ -95,8 +101,10 @@ export async function postUnitPreVerification(pctx: PostUnitContext): Promise<"d
   // Invalidate all caches
   invalidateAllCaches();
 
-  // Small delay to let files settle
-  await new Promise(r => setTimeout(r, 500));
+  // Small delay to let files settle (skipped for sidecars where latency matters more)
+  if (!opts?.skipSettleDelay) {
+    await new Promise(r => setTimeout(r, 100));
+  }
 
   // Auto-commit
   if (s.currentUnit) {
@@ -113,15 +121,25 @@ export async function postUnitPreVerification(pctx: PostUnitContext): Promise<"d
               const summaryContent = await loadFile(summaryPath);
               if (summaryContent) {
                 const summary = parseSummary(summaryContent);
+                // Look up GitHub issue number for commit linking
+                let ghIssueNumber: number | undefined;
+                try {
+                  const { getTaskIssueNumberForCommit } = await import("../github-sync/sync.js");
+                  ghIssueNumber = getTaskIssueNumberForCommit(s.basePath, mid, sid, tid) ?? undefined;
+                } catch {
+                  // GitHub sync not available — skip
+                }
+
                 taskContext = {
                   taskId: `${sid}/${tid}`,
                   taskTitle: summary.title?.replace(/^T\d+:\s*/, "") || tid,
                   oneLiner: summary.oneLiner || undefined,
                   keyFiles: summary.frontmatter.key_files?.filter(f => !f.includes("{{")) || undefined,
+                  issueNumber: ghIssueNumber,
                 };
               }
-            } catch {
-              // Non-fatal
+            } catch (e) {
+              debugLog("postUnit", { phase: "task-summary-parse", error: String(e) });
             }
           }
         }
@@ -131,12 +149,20 @@ export async function postUnitPreVerification(pctx: PostUnitContext): Promise<"d
       if (commitMsg) {
         ctx.ui.notify(`Committed: ${commitMsg.split("\n")[0]}`, "info");
       }
-    } catch {
-      // Non-fatal
+    } catch (e) {
+      debugLog("postUnit", { phase: "auto-commit", error: String(e) });
     }
 
-    // Doctor: fix mechanical bookkeeping
+    // GitHub sync (non-blocking, opt-in)
     try {
+      const { runGitHubSync } = await import("../github-sync/sync.js");
+      await runGitHubSync(s.basePath, s.currentUnit.type, s.currentUnit.id);
+    } catch (e) {
+      debugLog("postUnit", { phase: "github-sync", error: String(e) });
+    }
+
+    // Doctor: fix mechanical bookkeeping (skipped for lightweight sidecars)
+    if (!opts?.skipDoctor) try {
       const scopeParts = s.currentUnit.id.split("/").slice(0, 2);
       const doctorScope = scopeParts.join("/");
       const sliceTerminalUnits = new Set(["complete-slice", "run-uat"]);
@@ -146,13 +172,20 @@ export async function postUnitPreVerification(pctx: PostUnitContext): Promise<"d
         ctx.ui.notify(`Post-hook: applied ${report.fixesApplied.length} fix(es).`, "info");
       }
 
-      // Proactive health tracking
-      const summary = summarizeDoctorIssues(report.issues);
+      // Proactive health tracking — filter to current milestone to avoid
+      // cross-milestone stale errors inflating the escalation counter
+      const currentMilestoneId = s.currentUnit.id.split("/")[0];
+      const milestoneIssues = currentMilestoneId
+        ? report.issues.filter(i =>
+            i.unitId === currentMilestoneId ||
+            i.unitId.startsWith(`${currentMilestoneId}/`))
+        : report.issues;
+      const summary = summarizeDoctorIssues(milestoneIssues);
       recordHealthSnapshot(summary.errors, summary.warnings, report.fixesApplied.length);
 
       // Check if we should escalate to LLM-assisted heal
       if (summary.errors > 0) {
-        const unresolvedErrors = report.issues
+        const unresolvedErrors = milestoneIssues
           .filter(i => i.severity === "error" && !i.fixable)
           .map(i => ({ code: i.code, message: i.message, unitId: i.unitId }));
         const escalation = checkHealEscalation(summary.errors, unresolvedErrors);
@@ -168,24 +201,27 @@ export async function postUnitPreVerification(pctx: PostUnitContext): Promise<"d
             const reportText = formatDoctorReport(report, { scope: doctorScope, includeWarnings: true });
             const structuredIssues = formatDoctorIssuesForPrompt(actionable);
             dispatchDoctorHeal(pi, doctorScope, reportText, structuredIssues);
-          } catch {
-            // Non-fatal
+            return "dispatched";
+          } catch (e) {
+            debugLog("postUnit", { phase: "doctor-heal-dispatch", error: String(e) });
           }
         }
       }
-    } catch {
-      // Non-fatal
+    } catch (e) {
+      debugLog("postUnit", { phase: "doctor", error: String(e) });
     }
 
-    // Throttled STATE.md rebuild
-    const now = Date.now();
-    if (now - s.lastStateRebuildAt >= STATE_REBUILD_MIN_INTERVAL_MS) {
-      try {
-        await rebuildState(s.basePath);
-        s.lastStateRebuildAt = now;
-        autoCommitCurrentBranch(s.basePath, "state-rebuild", s.currentUnit.id);
-      } catch {
-        // Non-fatal
+    // Throttled STATE.md rebuild (skipped for lightweight sidecars)
+    if (!opts?.skipStateRebuild) {
+      const now = Date.now();
+      if (now - s.lastStateRebuildAt >= STATE_REBUILD_MIN_INTERVAL_MS) {
+        try {
+          await rebuildState(s.basePath);
+          s.lastStateRebuildAt = now;
+          autoCommitCurrentBranch(s.basePath, "state-rebuild", s.currentUnit.id);
+        } catch (e) {
+          debugLog("postUnit", { phase: "state-rebuild", error: String(e) });
+        }
       }
     }
 
@@ -193,16 +229,16 @@ export async function postUnitPreVerification(pctx: PostUnitContext): Promise<"d
     try {
       const { pruneDeadProcesses } = await import("../bg-shell/process-manager.js");
       pruneDeadProcesses();
-    } catch {
-      // Non-fatal
+    } catch (e) {
+      debugLog("postUnit", { phase: "prune-bg-shell", error: String(e) });
     }
 
-    // Sync worktree state back to project root
-    if (s.originalBasePath && s.originalBasePath !== s.basePath) {
+    // Sync worktree state back to project root (skipped for lightweight sidecars)
+    if (!opts?.skipWorktreeSync && s.originalBasePath && s.originalBasePath !== s.basePath) {
       try {
         syncStateToProjectRoot(s.basePath, s.originalBasePath, s.currentMilestoneId);
-      } catch {
-        // Non-fatal
+      } catch (e) {
+        debugLog("postUnit", { phase: "worktree-sync", error: String(e) });
       }
     }
 
@@ -210,10 +246,10 @@ export async function postUnitPreVerification(pctx: PostUnitContext): Promise<"d
     if (s.currentUnit.type === "rewrite-docs") {
       try {
         await resolveAllOverrides(s.basePath);
-        resetRewriteCircuitBreaker();
+        s.rewriteAttemptCount = 0;
         ctx.ui.notify("Override(s) resolved — rewrite-docs completed.", "info");
-      } catch {
-        // Non-fatal
+      } catch (e) {
+        debugLog("postUnit", { phase: "rewrite-docs-resolve", error: String(e) });
       }
     }
 
@@ -226,8 +262,8 @@ export async function postUnitPreVerification(pctx: PostUnitContext): Promise<"d
           const { clearReactiveState } = await import("./reactive-graph.js");
           clearReactiveState(s.basePath, mid, sid);
         }
-      } catch {
-        // Non-fatal
+      } catch (e) {
+        debugLog("postUnit", { phase: "reactive-state-cleanup", error: String(e) });
       }
     }
 
@@ -280,8 +316,8 @@ export async function postUnitPreVerification(pctx: PostUnitContext): Promise<"d
         if (triggerArtifactVerified) {
           invalidateAllCaches();
         }
-      } catch {
-        // Non-fatal
+      } catch (e) {
+        debugLog("postUnit", { phase: "artifact-verify", error: String(e) });
       }
     } else {
       // Hook unit completed — finalize its runtime record
@@ -292,8 +328,8 @@ export async function postUnitPreVerification(pctx: PostUnitContext): Promise<"d
           lastProgressKind: "hook-completed",
         });
         clearUnitRuntimeRecord(s.basePath, s.currentUnit.type, s.currentUnit.id);
-      } catch {
-        // Non-fatal
+      } catch (e) {
+        debugLog("postUnit", { phase: "hook-finalize", error: String(e) });
       }
     }
   }
@@ -429,8 +465,8 @@ export async function postUnitPostVerification(pctx: PostUnitContext): Promise<"
           }
         }
       }
-    } catch {
-      // Triage check failure is non-fatal
+    } catch (e) {
+      debugLog("postUnit", { phase: "triage-check", error: String(e) });
     }
   }
 
@@ -475,8 +511,8 @@ export async function postUnitPostVerification(pctx: PostUnitContext): Promise<"
       );
 
       return "continue";
-    } catch {
-      // Non-fatal — proceed to normal dispatch
+    } catch (e) {
+      debugLog("postUnit", { phase: "quick-task-dispatch", error: String(e) });
     }
   }
 

package/src/resources/extensions/gsd/auto-prompts.ts

@@ -20,11 +20,17 @@ import type { GSDState, InlineLevel } from "./types.js";
 import type { GSDPreferences } from "./preferences.js";
 import { join } from "node:path";
 import { existsSync } from "node:fs";
-import { computeBudgets, resolveExecutorContextWindow } from "./context-budget.js";
-import { compressToTarget } from "./prompt-compressor.js";
-import { distillSummaries } from "./summary-distiller.js";
+import { computeBudgets, resolveExecutorContextWindow, truncateAtSectionBoundary } from "./context-budget.js";
 import { formatDecisionsCompact, formatRequirementsCompact } from "./structured-data-formatter.js";
-import { chunkByRelevance, formatChunks } from "./semantic-chunker.js";
+
+// ─── Preamble Cap ─────────────────────────────────────────────────────────────
+
+const MAX_PREAMBLE_CHARS = 30_000;
+
+function capPreamble(preamble: string): string {
+  if (preamble.length <= MAX_PREAMBLE_CHARS) return preamble;
+  return truncateAtSectionBoundary(preamble, MAX_PREAMBLE_CHARS).content;
+}
 
 // ─── Executor Constraints ─────────────────────────────────────────────────────
 
@@ -159,16 +165,9 @@ export async function inlineFileSmart(
     return `### ${label}\nSource: \`${relPath}\`\n\n${content.trim()}`;
   }
 
-  // Use semantic chunking for large files
-  const result = chunkByRelevance(content, query, { maxChunks: 5, minScore: 0.05 });
-
-  // If chunking didn't save much (< 20%), just include full content
-  if (result.savingsPercent < 20) {
-    return `### ${label}\nSource: \`${relPath}\`\n\n${content.trim()}`;
-  }
-
-  const formatted = formatChunks(result, relPath);
-  return `### ${label} (${result.omittedChunks} sections omitted for relevance)\nSource: \`${relPath}\`\n\n${formatted}`;
+  // For large files, truncate at section boundary
+  const truncated = truncateAtSectionBoundary(content, threshold).content;
+  return `### ${label}\nSource: \`${relPath}\`\n\n${truncated}`;
 }
 
 /**
@@ -202,21 +201,6 @@ export async function inlineDependencySummaries(
 
   const result = sections.join("\n\n");
   if (budgetChars !== undefined && result.length > budgetChars) {
-    // For 3+ summaries, try distillation first (preserves more information)
-    if (sections.length >= 3) {
-      const rawSummaries = sections.map(s => {
-        // Extract content after the header line
-        const lines = s.split("\n");
-        const contentStart = lines.findIndex(l => l.startsWith("Source:"));
-        return contentStart >= 0 ? lines.slice(contentStart + 1).join("\n").trim() : s;
-      });
-      const distilled = distillSummaries(rawSummaries, budgetChars);
-      if (distilled.content.length <= budgetChars) {
-        return distilled.content;
-      }
-    }
-    // Fall back to section-boundary truncation
-    const { truncateAtSectionBoundary } = await import("./context-budget.js");
     return truncateAtSectionBoundary(result, budgetChars).content;
   }
   return result;
@@ -634,7 +618,7 @@ export async function buildResearchMilestonePrompt(mid: string, midTitle: string
   if (knowledgeInlineRM) inlined.push(knowledgeInlineRM);
   inlined.push(inlineTemplate("research", "Research"));
 
-  const inlinedContext = `## Inlined Context (preloaded — do not re-read these files)\n\n${inlined.join("\n\n---\n\n")}`;
+  const inlinedContext = capPreamble(`## Inlined Context (preloaded — do not re-read these files)\n\n${inlined.join("\n\n---\n\n")}`);
 
   const outputRelPath = relMilestoneFile(base, mid, "RESEARCH");
   return loadPrompt("research-milestone", {
@@ -684,7 +668,7 @@ export async function buildPlanMilestonePrompt(mid: string, midTitle: string, ba
     inlined.push(inlineTemplate("task-plan", "Task Plan"));
   }
 
-  const inlinedContext = `## Inlined Context (preloaded — do not re-read these files)\n\n${inlined.join("\n\n---\n\n")}`;
+  const inlinedContext = capPreamble(`## Inlined Context (preloaded — do not re-read these files)\n\n${inlined.join("\n\n---\n\n")}`);
 
   const outputRelPath = relMilestoneFile(base, mid, "ROADMAP");
   const researchOutputPath = join(base, relMilestoneFile(base, mid, "RESEARCH"));
@@ -733,7 +717,7 @@ export async function buildResearchSlicePrompt(
   const overridesInline = formatOverridesSection(activeOverrides);
   if (overridesInline) inlined.unshift(overridesInline);
 
-  const inlinedContext = `## Inlined Context (preloaded — do not re-read these files)\n\n${inlined.join("\n\n---\n\n")}`;
+  const inlinedContext = capPreamble(`## Inlined Context (preloaded — do not re-read these files)\n\n${inlined.join("\n\n---\n\n")}`);
 
   const outputRelPath = relSliceFile(base, mid, sid, "RESEARCH");
   return loadPrompt("research-slice", {
@@ -781,7 +765,7 @@ export async function buildPlanSlicePrompt(
   const planOverridesInline = formatOverridesSection(planActiveOverrides);
   if (planOverridesInline) inlined.unshift(planOverridesInline);
 
-  const inlinedContext = `## Inlined Context (preloaded — do not re-read these files)\n\n${inlined.join("\n\n---\n\n")}`;
+  const inlinedContext = capPreamble(`## Inlined Context (preloaded — do not re-read these files)\n\n${inlined.join("\n\n---\n\n")}`);
 
   // Build executor context constraints from the budget engine
   const executorContextConstraints = formatExecutorConstraints();
@@ -900,15 +884,11 @@ export async function buildExecuteTaskPrompt(
   const budgets = computeBudgets(contextWindow);
   const verificationBudget = `~${Math.round(budgets.verificationBudgetChars / 1000)}K chars`;
 
-  // Compress carry-forward section when it exceeds 40% of inline context budget.
-  // Only compress when compression_strategy is "compress" (budget/balanced profiles).
+  // Truncate carry-forward section when it exceeds 40% of inline context budget.
   const carryForwardBudget = Math.floor(budgets.inlineContextBudgetChars * 0.4);
   let finalCarryForward = carryForwardSection;
   if (carryForwardSection.length > carryForwardBudget) {
-    const { resolveCompressionStrategy } = await import("./preferences.js");
-    if (resolveCompressionStrategy() === "compress") {
-      finalCarryForward = compressToTarget(carryForwardSection, carryForwardBudget).content;
-    }
+    finalCarryForward = truncateAtSectionBoundary(carryForwardSection, carryForwardBudget).content;
   }
 
   return loadPrompt("execute-task", {
@@ -971,7 +951,7 @@ export async function buildCompleteSlicePrompt(
   const completeOverridesInline = formatOverridesSection(completeActiveOverrides);
   if (completeOverridesInline) inlined.unshift(completeOverridesInline);
 
-  const inlinedContext = `## Inlined Context (preloaded — do not re-read these files)\n\n${inlined.join("\n\n---\n\n")}`;
+  const inlinedContext = capPreamble(`## Inlined Context (preloaded — do not re-read these files)\n\n${inlined.join("\n\n---\n\n")}`);
 
   const sliceRel = relSlicePath(base, mid, sid);
   const sliceSummaryPath = join(base, `${sliceRel}/${sid}-SUMMARY.md`);
@@ -1030,7 +1010,7 @@ export async function buildCompleteMilestonePrompt(
   if (contextInline) inlined.push(contextInline);
   inlined.push(inlineTemplate("milestone-summary", "Milestone Summary"));
 
-  const inlinedContext = `## Inlined Context (preloaded — do not re-read these files)\n\n${inlined.join("\n\n---\n\n")}`;
+  const inlinedContext = capPreamble(`## Inlined Context (preloaded — do not re-read these files)\n\n${inlined.join("\n\n---\n\n")}`);
 
   const milestoneSummaryPath = join(base, `${relMilestonePath(base, mid)}/${mid}-SUMMARY.md`);
 
@@ -1101,7 +1081,7 @@ export async function buildValidateMilestonePrompt(
   const contextInline = await inlineFileOptional(contextPath, contextRel, "Milestone Context");
   if (contextInline) inlined.push(contextInline);
 
-  const inlinedContext = `## Inlined Context (preloaded — do not re-read these files)\n\n${inlined.join("\n\n---\n\n")}`;
+  const inlinedContext = capPreamble(`## Inlined Context (preloaded — do not re-read these files)\n\n${inlined.join("\n\n---\n\n")}`);
 
   const validationOutputPath = join(base, `${relMilestonePath(base, mid)}/${mid}-VALIDATION.md`);
   const roadmapOutputPath = `${relMilestonePath(base, mid)}/${mid}-ROADMAP.md`;
@@ -1155,7 +1135,7 @@ export async function buildReplanSlicePrompt(
   const replanOverridesInline = formatOverridesSection(replanActiveOverrides);
   if (replanOverridesInline) inlined.unshift(replanOverridesInline);
 
-  const inlinedContext = `## Inlined Context (preloaded — do not re-read these files)\n\n${inlined.join("\n\n---\n\n")}`;
+  const inlinedContext = capPreamble(`## Inlined Context (preloaded — do not re-read these files)\n\n${inlined.join("\n\n---\n\n")}`);
 
   const replanPath = join(base, `${relSlicePath(base, mid, sid)}/${sid}-REPLAN.md`);
 
@@ -1203,7 +1183,7 @@ export async function buildRunUatPrompt(
   const projectInline = await inlineProjectFromDb(base);
   if (projectInline) inlined.push(projectInline);
 
-  const inlinedContext = `## Inlined Context (preloaded — do not re-read these files)\n\n${inlined.join("\n\n---\n\n")}`;
+  const inlinedContext = capPreamble(`## Inlined Context (preloaded — do not re-read these files)\n\n${inlined.join("\n\n---\n\n")}`);
 
   const uatResultPath = join(base, relSliceFile(base, mid, sliceId, "UAT-RESULT"));
   const uatType = extractUatType(uatContent) ?? "human-experience";
@@ -1242,7 +1222,7 @@ export async function buildReassessRoadmapPrompt(
   const knowledgeInlineRA = await inlineGsdRootFile(base, "knowledge.md", "Project Knowledge");
   if (knowledgeInlineRA) inlined.push(knowledgeInlineRA);
 
-  const inlinedContext = `## Inlined Context (preloaded — do not re-read these files)\n\n${inlined.join("\n\n---\n\n")}`;
+  const inlinedContext = capPreamble(`## Inlined Context (preloaded — do not re-read these files)\n\n${inlined.join("\n\n---\n\n")}`);
 
   const assessmentPath = join(base, relSliceFile(base, mid, completedSliceId, "ASSESSMENT"));
 

package/src/resources/extensions/gsd/auto-start.ts

@@ -20,7 +20,7 @@ import {
   resolveSkillDiscoveryMode,
   getIsolationMode,
 } from "./preferences.js";
-import { ensureGsdSymlink } from "./repo-identity.js";
+import { ensureGsdSymlink, validateProjectId } from "./repo-identity.js";
 import { migrateToExternalState, recoverFailedMigration } from "./migrate-external.js";
 import { collectSecretsFromManifest } from "../get-secrets-from-user.js";
 import { gsdRoot, resolveMilestoneFile, milestonesDir } from "./paths.js";
@@ -130,6 +130,16 @@ export async function bootstrapAutoSession(
   }
 
   try {
+    // Validate GSD_PROJECT_ID early so the user gets immediate feedback
+    const customProjectId = process.env.GSD_PROJECT_ID;
+    if (customProjectId && !validateProjectId(customProjectId)) {
+      ctx.ui.notify(
+        `GSD_PROJECT_ID must contain only alphanumeric characters, hyphens, and underscores. Got: "${customProjectId}"`,
+        "error",
+      );
+      return releaseLockAndReturn();
+    }
+
     // Ensure git repo exists
     if (!nativeIsRepo(base)) {
       const mainBranch =
@@ -429,10 +439,16 @@ export async function bootstrapAutoSession(
     s.originalBasePath = base;
 
     const isUnderGsdWorktrees = (p: string): boolean => {
+      // Direct layout: /.gsd/worktrees/
       const marker = `${pathSep}.gsd${pathSep}worktrees${pathSep}`;
       if (p.includes(marker)) return true;
       const worktreesSuffix = `${pathSep}.gsd${pathSep}worktrees`;
-      return p.endsWith(worktreesSuffix);
+      if (p.endsWith(worktreesSuffix)) return true;
+      // Symlink-resolved layout: /.gsd/projects/<hash>/worktrees/
+      const symlinkRe = new RegExp(
+        `\\${pathSep}\\.gsd\\${pathSep}projects\\${pathSep}[a-f0-9]+\\${pathSep}worktrees(?:\\${pathSep}|$)`,
+      );
+      return symlinkRe.test(p);
     };
 
     if (

package/src/resources/extensions/gsd/auto-worktree-sync.ts

@@ -22,6 +22,8 @@ import { join, sep as pathSep } from "node:path";
 import { homedir } from "node:os";
 import { safeCopy, safeCopyRecursive } from "./safe-fs.js";
 
+const gsdHome = process.env.GSD_HOME || join(homedir(), ".gsd");
+
 // ─── Project Root → Worktree Sync ─────────────────────────────────────────
 
 /**
@@ -111,7 +113,7 @@ export function syncStateToProjectRoot(
  */
 export function readResourceVersion(): string | null {
   const agentDir =
-    process.env.GSD_CODING_AGENT_DIR || join(homedir(), ".gsd", "agent");
+    process.env.GSD_CODING_AGENT_DIR || join(gsdHome, "agent");
   const manifestPath = join(agentDir, "managed-resources.json");
   try {
     const manifest = JSON.parse(readFileSync(manifestPath, "utf-8"));
@@ -153,9 +155,18 @@ export function checkResourcesStale(
  * Returns the corrected base path.
  */
 export function escapeStaleWorktree(base: string): string {
-  const marker = `${pathSep}.gsd${pathSep}worktrees${pathSep}`;
-  const idx = base.indexOf(marker);
-  if (idx === -1) return base;
+  // Direct layout: /.gsd/worktrees/
+  const directMarker = `${pathSep}.gsd${pathSep}worktrees${pathSep}`;
+  let idx = base.indexOf(directMarker);
+  if (idx === -1) {
+    // Symlink-resolved layout: /.gsd/projects/<hash>/worktrees/
+    const symlinkRe = new RegExp(
+      `\\${pathSep}\\.gsd\\${pathSep}projects\\${pathSep}[a-f0-9]+\\${pathSep}worktrees\\${pathSep}`,
+    );
+    const match = base.match(symlinkRe);
+    if (!match || match.index === undefined) return base;
+    idx = match.index;
+  }
 
   // base is inside .gsd/worktrees/<something> — extract the project root
   const projectRoot = base.slice(0, idx);

package/src/resources/extensions/gsd/auto-worktree.ts

@@ -37,13 +37,13 @@ import {
   resolveGitHeadPath,
   nudgeGitBranchCache,
 } from "./worktree.js";
-import { MergeConflictError, readIntegrationBranch } from "./git-service.js";
+import { MergeConflictError, readIntegrationBranch, RUNTIME_EXCLUSION_PATHS } from "./git-service.js";
 import { parseRoadmap } from "./files.js";
 import { loadEffectiveGSDPreferences } from "./preferences.js";
 import {
   nativeGetCurrentBranch,
   nativeWorkingTreeStatus,
-  nativeAddAll,
+  nativeAddAllWithExclusions,
   nativeCommit,
   nativeCheckoutBranch,
   nativeMergeSquash,
@@ -768,7 +768,7 @@ function autoCommitDirtyState(cwd: string): boolean {
   try {
     const status = nativeWorkingTreeStatus(cwd);
     if (!status) return false;
-    nativeAddAll(cwd);
+    nativeAddAllWithExclusions(cwd, RUNTIME_EXCLUSION_PATHS);
     const result = nativeCommit(
       cwd,
       "chore: auto-commit before milestone merge",