fix(#2853): sync .sisyphus state from worktree to main repo before removal

When .sisyphus/ is gitignored, task state written during worktree execution
is lost when the worktree is removed. Fix:

- add worktree-sync.ts: syncSisyphusStateFromWorktree() copies .sisyphus/
  contents from worktree to main repo directory
- update start-work.ts template: documents the sync step as CRITICAL when
  worktree_path is set in boulder.json
- update work-with-pr/SKILL.md: adds explicit sync step before worktree removal
- export from boulder-state index
- test: 5 scenarios covering no-.sisyphus, nested dirs, overwrite stale state

.opencode/skills/work-with-pr/SKILL.md

@@ -282,6 +282,18 @@ Once all three gates pass:
 gh pr merge "$PR_NUMBER" --squash --delete-branch
 ```
 
+### Sync .sisyphus state back to main repo
+
+Before removing the worktree, copy `.sisyphus/` state back. When `.sisyphus/` is gitignored, files written there during worktree execution are not committed or merged — they would be lost on worktree removal.
+
+```bash
+# Sync .sisyphus state from worktree to main repo (preserves task state, plans, notepads)
+if [ -d "$WORKTREE_PATH/.sisyphus" ]; then
+  mkdir -p "$ORIGINAL_DIR/.sisyphus"
+  cp -r "$WORKTREE_PATH/.sisyphus/"* "$ORIGINAL_DIR/.sisyphus/" 2>/dev/null || true
+fi
+```
+
 ### Clean up the worktree
 
 The worktree served its purpose — remove it to avoid disk bloat:

src/features/boulder-state/index.ts

@@ -2,3 +2,4 @@ export * from "./types"
 export * from "./constants"
 export * from "./storage"
 export * from "./top-level-task"
+export * from "./worktree-sync"

src/features/boulder-state/worktree-sync.test.ts

@@ -0,0 +1,88 @@
+import { describe, expect, test, beforeEach, afterEach } from "bun:test"
+import { existsSync, mkdirSync, rmSync, writeFileSync, readFileSync } from "node:fs"
+import { join } from "node:path"
+import { tmpdir } from "node:os"
+import { syncSisyphusStateFromWorktree } from "./worktree-sync"
+
+describe("syncSisyphusStateFromWorktree", () => {
+  const BASE = join(tmpdir(), "worktree-sync-test-" + Date.now())
+  const WORKTREE = join(BASE, "worktree")
+  const MAIN_REPO = join(BASE, "main")
+
+  beforeEach(() => {
+    mkdirSync(WORKTREE, { recursive: true })
+    mkdirSync(MAIN_REPO, { recursive: true })
+  })
+
+  afterEach(() => {
+    if (existsSync(BASE)) {
+      rmSync(BASE, { recursive: true, force: true })
+    }
+  })
+
+  test("#given no .sisyphus in worktree #when syncing #then returns true without error", () => {
+    const result = syncSisyphusStateFromWorktree(WORKTREE, MAIN_REPO)
+
+    expect(result).toBe(true)
+    expect(existsSync(join(MAIN_REPO, ".sisyphus"))).toBe(false)
+  })
+
+  test("#given .sisyphus with boulder.json in worktree #when syncing #then copies to main repo", () => {
+    const worktreeSisyphus = join(WORKTREE, ".sisyphus")
+    mkdirSync(worktreeSisyphus, { recursive: true })
+    writeFileSync(join(worktreeSisyphus, "boulder.json"), '{"active_plan":"/plan.md","plan_name":"test"}')
+
+    const result = syncSisyphusStateFromWorktree(WORKTREE, MAIN_REPO)
+
+    expect(result).toBe(true)
+    const copied = readFileSync(join(MAIN_REPO, ".sisyphus", "boulder.json"), "utf-8")
+    expect(JSON.parse(copied).plan_name).toBe("test")
+  })
+
+  test("#given nested .sisyphus dirs in worktree #when syncing #then copies full tree recursively", () => {
+    const worktreePlans = join(WORKTREE, ".sisyphus", "plans")
+    const worktreeNotepads = join(WORKTREE, ".sisyphus", "notepads", "my-plan")
+    mkdirSync(worktreePlans, { recursive: true })
+    mkdirSync(worktreeNotepads, { recursive: true })
+    writeFileSync(join(worktreePlans, "my-plan.md"), "- [x] Task 1\n- [ ] Task 2")
+    writeFileSync(join(worktreeNotepads, "learnings.md"), "learned something")
+
+    const result = syncSisyphusStateFromWorktree(WORKTREE, MAIN_REPO)
+
+    expect(result).toBe(true)
+    expect(readFileSync(join(MAIN_REPO, ".sisyphus", "plans", "my-plan.md"), "utf-8")).toContain("Task 1")
+    expect(readFileSync(join(MAIN_REPO, ".sisyphus", "notepads", "my-plan", "learnings.md"), "utf-8")).toBe("learned something")
+  })
+
+  test("#given existing .sisyphus in main repo #when syncing #then worktree state overwrites stale state", () => {
+    const mainSisyphus = join(MAIN_REPO, ".sisyphus")
+    mkdirSync(mainSisyphus, { recursive: true })
+    writeFileSync(join(mainSisyphus, "boulder.json"), '{"plan_name":"old"}')
+
+    const worktreeSisyphus = join(WORKTREE, ".sisyphus")
+    mkdirSync(worktreeSisyphus, { recursive: true })
+    writeFileSync(join(worktreeSisyphus, "boulder.json"), '{"plan_name":"updated"}')
+
+    const result = syncSisyphusStateFromWorktree(WORKTREE, MAIN_REPO)
+
+    expect(result).toBe(true)
+    const content = readFileSync(join(mainSisyphus, "boulder.json"), "utf-8")
+    expect(JSON.parse(content).plan_name).toBe("updated")
+  })
+
+  test("#given pre-existing files in main .sisyphus #when syncing #then preserves files not in worktree", () => {
+    const mainSisyphus = join(MAIN_REPO, ".sisyphus", "rules")
+    mkdirSync(mainSisyphus, { recursive: true })
+    writeFileSync(join(mainSisyphus, "my-rule.md"), "existing rule")
+
+    const worktreeSisyphus = join(WORKTREE, ".sisyphus")
+    mkdirSync(worktreeSisyphus, { recursive: true })
+    writeFileSync(join(worktreeSisyphus, "boulder.json"), '{"plan_name":"new"}')
+
+    const result = syncSisyphusStateFromWorktree(WORKTREE, MAIN_REPO)
+
+    expect(result).toBe(true)
+    expect(readFileSync(join(MAIN_REPO, ".sisyphus", "rules", "my-rule.md"), "utf-8")).toBe("existing rule")
+    expect(existsSync(join(MAIN_REPO, ".sisyphus", "boulder.json"))).toBe(true)
+  })
+})

src/features/boulder-state/worktree-sync.ts

@@ -0,0 +1,34 @@
+import { existsSync, cpSync, mkdirSync } from "node:fs"
+import { join } from "node:path"
+import { BOULDER_DIR } from "./constants"
+import { log } from "../../shared/logger"
+
+export function syncSisyphusStateFromWorktree(worktreePath: string, mainRepoPath: string): boolean {
+  const srcDir = join(worktreePath, BOULDER_DIR)
+  const destDir = join(mainRepoPath, BOULDER_DIR)
+
+  if (!existsSync(srcDir)) {
+    log("[worktree-sync] No .sisyphus directory in worktree, nothing to sync", { worktreePath })
+    return true
+  }
+
+  try {
+    if (!existsSync(destDir)) {
+      mkdirSync(destDir, { recursive: true })
+    }
+
+    cpSync(srcDir, destDir, { recursive: true, force: true })
+    log("[worktree-sync] Synced .sisyphus state from worktree to main repo", {
+      worktreePath,
+      mainRepoPath,
+    })
+    return true
+  } catch (err) {
+    log("[worktree-sync] Failed to sync .sisyphus state", {
+      worktreePath,
+      mainRepoPath,
+      error: String(err),
+    })
+    return false
+  }
+}

src/features/builtin-commands/templates/start-work.ts

@@ -115,9 +115,14 @@ Register these as task/todo items so progress is tracked and visible throughout
 
 When working in a worktree (\`worktree_path\` is set in boulder.json) and ALL plan tasks are complete:
 1. Commit all remaining changes in the worktree
-2. Switch to the main working directory (the original repo, NOT the worktree)
-3. Merge the worktree branch into the current branch: \`git merge <worktree-branch>\`
-4. If merge succeeds, clean up: \`git worktree remove <worktree-path>\`
-5. Remove the boulder.json state
+2. **Sync .sisyphus state back**: Copy \`.sisyphus/\` from the worktree to the main repo before removal.
+   This is CRITICAL when \`.sisyphus/\` is gitignored — state written during worktree execution would otherwise be lost.
+   \`\`\`bash
+   cp -r <worktree-path>/.sisyphus/* <main-repo>/.sisyphus/ 2>/dev/null || true
+   \`\`\`
+3. Switch to the main working directory (the original repo, NOT the worktree)
+4. Merge the worktree branch into the current branch: \`git merge <worktree-branch>\`
+5. If merge succeeds, clean up: \`git worktree remove <worktree-path>\`
+6. Remove the boulder.json state
 
 This is the DEFAULT behavior when \`--worktree\` was used. Skip merge only if the user explicitly instructs otherwise (e.g., asks to create a PR instead).`