Merge pull request #3557 from Tibsfox/fix/rethink-skip-slice-db-sync

fix(gsd): rebuild STATE.md after skip-slice and strengthen rethink prompt

src/resources/extensions/gsd/bootstrap/db-tools.ts

@@ -1000,6 +1000,16 @@ export function registerDbTools(pi: ExtensionAPI): void {
       updateSliceStatus(params.milestoneId, params.sliceId, "skipped");
       invalidateStateCache();
 
+      // Rebuild STATE.md so it reflects the skip immediately (#3477).
+      // Without this, /gsd auto reads stale STATE.md and resumes the skipped slice.
+      try {
+        const basePath = process.cwd();
+        const { rebuildState } = await import("../doctor.js");
+        await rebuildState(basePath);
+      } catch (err) {
+        logError("tool", `skip_slice rebuildState failed: ${(err as Error).message}`, { tool: "gsd_skip_slice" });
+      }
+
       return {
         content: [{ type: "text" as const, text: `Skipped slice ${params.sliceId} (${params.milestoneId}). Reason: ${params.reason ?? "User-directed skip"}. Auto-mode will advance past this slice.` }],
         details: {

src/resources/extensions/gsd/prompts/rethink.md

@@ -46,11 +46,12 @@ reason: "<reason>"
 Remove the `{ID}-PARKED.md` file from the milestone directory to reactivate it.
 
 ### Skip a slice
-Mark a slice as skipped so auto-mode advances past it without executing. Use the `gsd_skip_slice` tool:
+Mark a slice as skipped so auto-mode advances past it without executing. **You MUST call the `gsd_skip_slice` tool** — editing the roadmap markdown alone is NOT sufficient because auto-mode reads slice status from the database, not the roadmap file:
 ```
 gsd_skip_slice({ milestoneId: "M003", sliceId: "S02", reason: "Descoped — feature moved to M005" })
 ```
 Skipped slices are treated as closed by the state machine (like "complete" but distinct). Use when a slice is no longer needed or has been superseded. The slice data is preserved for reference.
+**Do NOT** just check the slice checkbox in the roadmap — this does not update the DB and auto-mode will resume the slice.
 
 ### Discard a milestone
 **Permanently** delete a milestone directory and prune it from QUEUE-ORDER.json. **Always confirm with the user before discarding.** Warn explicitly if the milestone has completed work.

src/resources/extensions/gsd/tests/skip-slice-state-rebuild.test.ts

@@ -0,0 +1,31 @@
+/**
+ * Regression test for #3477: gsd_skip_slice tool must rebuild STATE.md
+ * after updating the DB so auto-mode reads the correct state.
+ */
+import { test } from "node:test";
+import assert from "node:assert/strict";
+import { readFileSync } from "node:fs";
+import { join } from "node:path";
+
+test("gsd_skip_slice tool calls rebuildState after DB update (#3477)", () => {
+  const src = readFileSync(
+    join(import.meta.dirname, "..", "bootstrap", "db-tools.ts"),
+    "utf-8",
+  );
+  // The fix adds a rebuildState call after updateSliceStatus in skip_slice
+  assert.ok(
+    src.includes("rebuildState"),
+    "gsd_skip_slice must call rebuildState after updating slice status",
+  );
+});
+
+test("rethink prompt warns against markdown-only edits for skip (#3477)", () => {
+  const prompt = readFileSync(
+    join(import.meta.dirname, "..", "prompts", "rethink.md"),
+    "utf-8",
+  );
+  assert.ok(
+    prompt.includes("MUST") && prompt.includes("gsd_skip_slice"),
+    "Rethink prompt must emphasize gsd_skip_slice tool requirement",
+  );
+});