cherry-pick(auto): handle worktree context fallback + sanitize paused session paths

Cherry-pick of gsd-build/gsd-2 a4f78731f — handles worktree context fallback
and sanitizes paths in paused session resumption. Skips uok-plan-v2-wiring
test hunk (drifted in sf).

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

src/resources/extensions/sf/auto.ts

@@ -127,7 +127,7 @@ import {
 } from "./metrics.js";
 import { setLogBasePath, logWarning, logError } from "./workflow-logger.js";
 import { homedir } from "node:os";
-import { join } from "node:path";
+import { isAbsolute, join } from "node:path";
 import { pathToFileURL } from "node:url";
 import { readFileSync, existsSync, mkdirSync, writeFileSync, unlinkSync } from "node:fs";
 import { atomicWriteSync } from "./atomic-write.js";
@@ -307,6 +307,21 @@ function restoreMilestoneLockEnv(): void {
   s.milestoneLockEnvCaptured = false;
 }
 
+function normalizeSessionFilePath(raw: unknown): string | null {
+  if (typeof raw !== "string") return null;
+  const trimmed = raw.trim();
+  if (!trimmed) return null;
+  const firstLine = trimmed.split(/\r?\n/, 1)[0]?.trim() ?? "";
+  if (!firstLine) return null;
+
+  // Guard against accidental message concatenation by trimming to .jsonl.
+  const jsonlIndex = firstLine.toLowerCase().indexOf(".jsonl");
+  const candidate = jsonlIndex >= 0 ? firstLine.slice(0, jsonlIndex + ".jsonl".length) : firstLine;
+  if (!isAbsolute(candidate)) return null;
+  if (!candidate.toLowerCase().endsWith(".jsonl")) return null;
+  return candidate;
+}
+
 export function startAutoDetached(
   ctx: ExtensionCommandContext,
   pi: ExtensionAPI,
@@ -1070,7 +1085,7 @@ export async function pauseAuto(
   // from provider-error pause and avoid hard-stopping (#2762).
   resolveAgentEndCancelled(_errorContext);
 
-  s.pausedSessionFile = ctx?.sessionManager?.getSessionFile() ?? null;
+  s.pausedSessionFile = normalizeSessionFilePath(ctx?.sessionManager?.getSessionFile() ?? null);
 
   // Persist paused-session metadata so resume survives /exit (#1383).
   // The fresh-start bootstrap checks for this file and restores worktree context.
@@ -1371,7 +1386,11 @@ export async function startAuto(
         s.autoStartTime = meta.autoStartTime || Date.now();
         s.sessionMilestoneLock = meta.milestoneLock ?? null;
         s.paused = true;
-        try { unlinkSync(pausedPath); } catch (e) { logWarning("session", `pause file cleanup failed: ${e instanceof Error ? e.message : String(e)}`, { file: "auto.ts" }); }
+        try { unlinkSync(pausedPath); } catch (e) {
+          if ((e as NodeJS.ErrnoException).code !== "ENOENT") {
+            logWarning("session", `pause file cleanup failed: ${e instanceof Error ? e.message : String(e)}`, { file: "auto.ts" });
+          }
+        }
         ctx.ui.notify(
           `Resuming paused custom workflow${meta.activeRunDir ? ` (${meta.activeRunDir})` : ""}.`,
           "info",
@@ -1390,7 +1409,9 @@ export async function startAuto(
           const summaryFile = resolveMilestoneFile(base, meta.milestoneId, "SUMMARY");
           if (!mDir || summaryFile) {
             try { unlinkSync(pausedPath); } catch (err) {
-              logWarning("session", `pause file cleanup failed: ${err instanceof Error ? err.message : String(err)}`, { file: "auto.ts" });
+              if ((err as NodeJS.ErrnoException).code !== "ENOENT") {
+                logWarning("session", `pause file cleanup failed: ${err instanceof Error ? err.message : String(err)}`, { file: "auto.ts" });
+              }
             }
             ctx.ui.notify(
               `Paused milestone ${meta.milestoneId} is ${!mDir ? "missing" : "already complete"}. Starting fresh.`,
@@ -1400,20 +1421,28 @@ export async function startAuto(
             s.currentMilestoneId = meta.milestoneId;
             s.originalBasePath = meta.originalBasePath || base;
             s.stepMode = meta.stepMode ?? requestedStepMode;
-            s.pausedSessionFile = meta.sessionFile ?? null;
+            s.pausedSessionFile = normalizeSessionFilePath(meta.sessionFile ?? null);
             s.pausedUnitType = meta.unitType ?? null;
             s.pausedUnitId = meta.unitId ?? null;
             s.autoStartTime = meta.autoStartTime || Date.now();
             s.sessionMilestoneLock = meta.milestoneLock ?? null;
             s.paused = true;
-            try { unlinkSync(pausedPath); } catch (e) { logWarning("session", `pause file cleanup failed: ${e instanceof Error ? e.message : String(e)}`, { file: "auto.ts" }); }
+            try { unlinkSync(pausedPath); } catch (e) {
+              if ((e as NodeJS.ErrnoException).code !== "ENOENT") {
+                logWarning("session", `pause file cleanup failed: ${e instanceof Error ? e.message : String(e)}`, { file: "auto.ts" });
+              }
+            }
             ctx.ui.notify(
               `Resuming paused session for ${meta.milestoneId}${meta.worktreePath && existsSync(meta.worktreePath) ? ` (worktree)` : ""}.`,
               "info",
             );
           }
         } else if (existsSync(pausedPath)) {
-          try { unlinkSync(pausedPath); } catch (e) { logWarning("session", `stale pause file cleanup failed: ${e instanceof Error ? e.message : String(e)}`, { file: "auto.ts" }); }
+          try { unlinkSync(pausedPath); } catch (e) {
+            if ((e as NodeJS.ErrnoException).code !== "ENOENT") {
+              logWarning("session", `stale pause file cleanup failed: ${e instanceof Error ? e.message : String(e)}`, { file: "auto.ts" });
+            }
+          }
         }
       }
     } catch (err) {
@@ -1472,7 +1501,9 @@ export async function startAuto(
     // Lock acquired — now safe to delete the pause file
     if (s.pausedSessionFile) {
       try { unlinkSync(s.pausedSessionFile); } catch (err) {
-        logWarning("session", `pause file cleanup failed: ${err instanceof Error ? err.message : String(err)}`, { file: "auto.ts" });
+        if ((err as NodeJS.ErrnoException).code !== "ENOENT") {
+          logWarning("session", `pause file cleanup failed: ${err instanceof Error ? err.message : String(err)}`, { file: "auto.ts" });
+        }
       }
       s.pausedSessionFile = null;
     }
@@ -1801,12 +1832,12 @@ export async function dispatchHookUnit(
     }
   }
 
-  const sessionFile = ctx.sessionManager.getSessionFile();
+  const sessionFile = normalizeSessionFilePath(ctx.sessionManager.getSessionFile());
   writeLock(
     lockBase(),
     hookUnitType,
     triggerUnitId,
-    sessionFile,
+    sessionFile ?? undefined,
   );
 
   clearUnitTimeout();

src/resources/extensions/sf/tests/auto-paused-session-validation.test.ts

@@ -39,6 +39,18 @@ test("auto.ts validates milestone before restoring paused session (#1664)", () =
     source.includes('resolveMilestoneFile(base, meta.milestoneId, "SUMMARY")'),
     "auto.ts must check for SUMMARY file to detect completed milestones",
   );
+
+  // Resume path must sanitize paused session file metadata before unlink/recovery.
+  assert.ok(
+    source.includes("normalizeSessionFilePath(meta.sessionFile ?? null)"),
+    "auto.ts must sanitize paused-session metadata sessionFile before using it",
+  );
+
+  // Pause path must sanitize live session file path before persisting metadata.
+  assert.ok(
+    source.includes("normalizeSessionFilePath(ctx?.sessionManager?.getSessionFile() ?? null)"),
+    "auto.ts must sanitize sessionManager getSessionFile output before persisting",
+  );
 });
 
 // ─── Filesystem validation unit tests ───────────────────────────────────────

src/resources/extensions/sf/uok/plan-v2.ts

@@ -42,6 +42,29 @@ function hasFileContent(path: string | null): boolean {
   }
 }
 
+function getArtifactLookupBases(basePath: string): string[] {
+  const bases = [basePath];
+  const projectRoot = process.env.GSD_PROJECT_ROOT;
+  if (projectRoot && projectRoot.trim().length > 0 && projectRoot !== basePath) {
+    bases.push(projectRoot);
+  }
+  return bases;
+}
+
+function hasMilestoneFileContent(
+  basePath: string,
+  milestoneId: string,
+  suffix: string,
+): boolean {
+  const bases = getArtifactLookupBases(basePath);
+  for (const candidateBase of bases) {
+    if (hasFileContent(resolveMilestoneFile(candidateBase, milestoneId, suffix))) {
+      return true;
+    }
+  }
+  return false;
+}
+
 function countSliceResearchArtifacts(basePath: string, milestoneId: string, slices: SliceRow[]): number {
   let count = 0;
   for (const slice of slices) {
@@ -60,9 +83,9 @@ export function compileUnitGraphFromState(basePath: string, state: SFState): Pla
   const slices = getMilestoneSlices(mid).sort((a, b) => Number(a.sequence ?? 0) - Number(b.sequence ?? 0));
   const nodes: UokGraphNode[] = [];
   const clarifyRoundLimit = PLAN_V2_CLARIFY_ROUND_LIMIT;
-  const draftContextIncluded = hasFileContent(resolveMilestoneFile(basePath, mid, "CONTEXT-DRAFT"));
-  const finalizedContextIncluded = hasFileContent(resolveMilestoneFile(basePath, mid, "CONTEXT"));
-  const researchSynthesized = hasFileContent(resolveMilestoneFile(basePath, mid, "RESEARCH"))
+  const draftContextIncluded = hasMilestoneFileContent(basePath, mid, "CONTEXT-DRAFT");
+  const finalizedContextIncluded = hasMilestoneFileContent(basePath, mid, "CONTEXT");
+  const researchSynthesized = hasMilestoneFileContent(basePath, mid, "RESEARCH")
     || countSliceResearchArtifacts(basePath, mid, slices) > 0;
 
   if (isExecutionEntryPhase(state.phase) && !finalizedContextIncluded) {