fix(workspaces): make managed runtimes reliable across restarts (#11740)

## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work
> - Execution workspaces need isolated databases, ports, and runtime
services
> - Concurrent workspaces could reuse ports or lose service ownership
after a restart
> - A markerless worktree also needed seed recovery, but normal
markerless instances still needed to boot
> - This pull request makes seed, port, and service ownership state
explicit and recoverable
> - It also checks live process and listener identity before it reclaims
shared resources
> - The benefit is reliable workspace startup, restart, adoption, and
concurrent provisioning

## Linked Issues or Issue Description

**What happened?**

Managed workspaces could lose runtime service ownership after a
control-plane restart. Concurrent worktrees could also reuse a port when
their parent paths differed. A seed recovery change made every
markerless instance resolve a worktree seed source, so normal instances
without a source could not start.

**Expected behavior**

Paperclip must preserve healthy managed services across restarts. It
must reserve unique ports across worktree parents. It must provision a
registered markerless worktree, but it must skip seed work for a normal
markerless instance.

**Steps to reproduce**

1. Start two managed worktrees under different parent paths at the same
time.
2. Restart the control plane while a managed service stays alive.
3. Start Paperclip with a config that has no seed markers and no
registered worktree source.
4. Observe duplicate port selection, lost service adoption, or a
seed-source startup error.

**Paperclip version or commit**

Current `master` plus the workspace runtime reliability changes in this
pull request.

**Deployment mode**

Local development with managed execution workspaces and embedded
Postgres.

## What Changed

- Added a shared port registry with lease heartbeats, process identity
checks, and live listener probes.
- Reserved worktree ports across custom parent paths and repaired
duplicate legacy assignments.
- Preserved and adopted healthy managed services across control-plane
restarts.
- Reconciled guest bind modes and verified listener ownership before
termination or reuse.
- Provisioned registered markerless worktree databases and kept normal
markerless instance startup as a no-op.
- Added CLI, shared, server, and shell regression tests for seed, port,
listener, restart, and adoption behavior.
- Updated the worktree development documentation.

## Verification

- `pnpm exec vitest run cli/src/__tests__/worktree.test.ts
--reporter=verbose` — 63 tests passed.
- `pnpm exec vitest run
packages/shared/src/worktree-port-registry.test.ts --reporter=verbose` —
5 tests passed.
- Focused runtime Vitest set — 199 tests passed across 37 suites.
- `node --test scripts/__tests__/provision-worktree-self-heal.test.mjs`
— 10 tests passed.
- `git diff --check` passed.

## Risks

- Port reservation now depends on lease and process identity data. The
fallback listener probe prevents early reclamation when process metadata
is incomplete.
- Runtime adoption is stricter about bind and owner identity. The tests
cover healthy adoption, stale records, PID reuse, and unrelated
listeners.
- Markerless seed detection now separates registered worktrees from
normal instances. The tests cover both paths.
- There are no database schema migrations.

> For core feature work, check [`ROADMAP.md`](ROADMAP.md) first and
discuss it in `#dev` before opening the PR. Feature PRs that overlap
with planned core work may need to be redirected — check the roadmap
first. See `CONTRIBUTING.md`.

## Model Used

- OpenAI Codex with the `gpt-5` model family. The serving snapshot and
context-window size are not exposed. The agent used reasoning,
repository tools, code execution, and test execution.

## Checklist

- [x] I have included a thinking path that traces from project context
to this change
- [x] I have specified the model used (with version and capability
details)
- [x] I have checked ROADMAP.md and confirmed this PR does not duplicate
planned core work
- [x] I have searched GitHub for duplicate or related PRs and linked
them above
- [x] I have either (a) linked existing issues with `Fixes: #` / `Closes
#` / `Refs #` OR (b) described the issue in-PR following the relevant
issue template
- [x] I have not referenced internal/instance-local Paperclip issues or
links (only public GitHub `#NNN` / `github.com/paperclipai/paperclip`
URLs)
- [x] My branch name describes the change (e.g. `docs/...`, `fix/...`)
and contains no internal Paperclip ticket id or instance-derived details
- [x] I have run tests locally and they pass
- [x] I have added or updated tests where applicable
- [x] I have updated relevant documentation to reflect my changes
- [x] I have considered and documented any risks above
- [x] All Paperclip CI gates are green
- [x] Greptile is 5/5 with no open P2s, recommendations, or follow-ups
- [x] I will address all Greptile and reviewer comments before
requesting merge

---------

Co-authored-by: Paperclip <noreply@paperclip.ing>
Co-authored-by: Dev Agent <dev@paperclip.ing>

scripts/__tests__/provision-worktree-self-heal.test.mjs

@@ -71,7 +71,21 @@ if (cliArgs[0] === "worktree" && cliArgs[1] === "ensure-seeded") {
     process.exit(${ensureExit});
   }
   fs.rmSync(".paperclip/seed-pending", { force: true });
-  fs.writeFileSync(".paperclip/seed-complete", "{}\\n");
+  fs.rmSync(".paperclip/seed-complete", { force: true });
+  fs.writeFileSync(".paperclip/seed-manifest.json", JSON.stringify({
+    version: 2,
+    source: { instanceId: "base-source", configPath: ${JSON.stringify(path.join(baseCwd, ".paperclip", "config.json"))} },
+    snapshotAt: "2026-08-19T00:00:00.000Z",
+    seedMode: "minimal",
+    migrationRevision: "0142_test.sql",
+    targetInstanceId: "target-test",
+    phase: "complete",
+    state: "verified",
+    attemptId: "attempt-test",
+    startedAt: "2026-08-19T00:00:00.000Z",
+    finishedAt: "2026-08-19T00:01:00.000Z",
+    diagnostics: [{ phase: "complete", status: "succeeded", at: "2026-08-19T00:01:00.000Z" }],
+  }) + "\\n");
   process.exit(0);
 }
 process.exit(0);
@@ -182,6 +196,45 @@ test("falls back to an isolated config when the base CLI cannot boot", () => {
   );
 });
 
+test("reconciles deployment mode from the registered source when reusing a guest config", () => {
+  const baseCwd = makeBaseWorkspace({ helpExit: 1, initExit: 0 });
+  const { result: first, worktreeCwd, worktreesHome } = runProvision(baseCwd);
+  assert.equal(first.status, 0, first.stderr);
+  assert.equal(readWorktreeConfig(worktreeCwd).server.deploymentMode, "local_trusted");
+
+  fs.writeFileSync(
+    path.join(baseCwd, ".paperclip", "config.json"),
+    `${JSON.stringify({
+      server: {
+        deploymentMode: "authenticated",
+        exposure: "private",
+      },
+    }, null, 2)}\n`,
+  );
+
+  const second = spawnSync("bash", [script], {
+    cwd: worktreeCwd,
+    encoding: "utf8",
+    env: {
+      PATH: testPath,
+      HOME: os.homedir(),
+      PAPERCLIP_WORKSPACE_BASE_CWD: baseCwd,
+      PAPERCLIP_WORKSPACE_CWD: worktreeCwd,
+      PAPERCLIP_WORKSPACE_BRANCH: "feature/provision-test",
+      PAPERCLIP_WORKTREES_DIR: worktreesHome,
+      PAPERCLIP_HOME: path.join(worktreesHome, "no-such-instance-home"),
+      PAPERCLIP_PROJECT_WORKSPACE_ID: "project-workspace-1",
+      PAPERCLIP_SEED_EXPECTED_COMPANY_ID: "company-1",
+    },
+  });
+
+  assert.equal(second.status, 0, second.stderr);
+  assert.match(second.stderr, /Reusing existing isolated Paperclip worktree config/);
+  assert.match(second.stderr, /Reconciled isolated Paperclip worktree deployment mode/);
+  assert.equal(readWorktreeConfig(worktreeCwd).server.deploymentMode, "authenticated");
+  assert.equal(readWorktreeConfig(worktreeCwd).server.exposure, "private");
+});
+
 test("repairs an unhealthy base install under the lock and then uses the CLI", (t) => {
   const hasTools = ["flock", "git"].every(
     (tool) => spawnSync("bash", ["-lc", `command -v ${tool}`], { env: { PATH: testPath } }).status === 0,
@@ -276,7 +329,10 @@ test("runtime provisioning invokes ensure-seeded once and fast-exits after succe
 
   const first = runRuntimeProvision(baseCwd, worktreeCwd);
   assert.equal(first.status, 0, first.stderr);
-  assert.ok(fs.existsSync(path.join(worktreeCwd, ".paperclip", "seed-complete")));
+  assert.equal(
+    JSON.parse(fs.readFileSync(path.join(worktreeCwd, ".paperclip", "seed-manifest.json"), "utf8")).state,
+    "verified",
+  );
   assert.ok(!fs.existsSync(path.join(worktreeCwd, ".paperclip", "seed-pending")));
 
   const ensureCallsAfterFirst = readCliInvocations(baseCwd)
@@ -287,12 +343,58 @@ test("runtime provisioning invokes ensure-seeded once and fast-exits after succe
 
   const second = runRuntimeProvision(baseCwd, worktreeCwd);
   assert.equal(second.status, 0, second.stderr);
-  assert.match(second.stderr, /already seeded.*skipping/);
+  assert.match(second.stderr, /verified seed manifest.*skipping/);
   const ensureCallsAfterSecond = readCliInvocations(baseCwd)
     .filter((args) => args[0] === "worktree" && args[1] === "ensure-seeded");
   assert.equal(ensureCallsAfterSecond.length, 1);
 });
 
+test("runtime provisioning seeds a worktree config that has no seed markers", () => {
+  const baseCwd = makeBaseWorkspace({ helpExit: 0, initExit: 0 });
+  const worktreeCwd = makeTempDir("paperclip-provision-runtime-unmarked-config-");
+  fs.mkdirSync(path.join(worktreeCwd, ".paperclip"), { recursive: true });
+  fs.writeFileSync(path.join(worktreeCwd, ".paperclip", "config.json"), "{}\n");
+
+  const result = runRuntimeProvision(baseCwd, worktreeCwd);
+
+  assert.equal(result.status, 0, result.stderr);
+  assert.equal(
+    readCliInvocations(baseCwd)
+      .filter((args) => args[0] === "worktree" && args[1] === "ensure-seeded").length,
+    1,
+  );
+  assert.equal(
+    JSON.parse(fs.readFileSync(path.join(worktreeCwd, ".paperclip", "seed-manifest.json"), "utf8")).state,
+    "verified",
+  );
+});
+
+test("runtime provisioning bootstraps and seeds an empty .paperclip directory", () => {
+  const baseCwd = makeBaseWorkspace({ helpExit: 0, initExit: 0 });
+  fs.mkdirSync(path.join(baseCwd, "scripts"), { recursive: true });
+  fs.copyFileSync(script, path.join(baseCwd, "scripts", "provision-worktree.sh"));
+  const worktreeCwd = makeTempDir("paperclip-provision-runtime-empty-state-");
+  fs.mkdirSync(path.join(worktreeCwd, ".paperclip"), { recursive: true });
+
+  const result = runRuntimeProvision(baseCwd, worktreeCwd);
+
+  assert.equal(result.status, 0, result.stderr);
+  assert.match(result.stderr, /config is missing; running the built-in worktree provisioner/);
+  const invocations = readCliInvocations(baseCwd);
+  assert.equal(
+    invocations.filter((args) => args[0] === "worktree" && args[1] === "init").length,
+    1,
+  );
+  assert.equal(
+    invocations.filter((args) => args[0] === "worktree" && args[1] === "ensure-seeded").length,
+    1,
+  );
+  assert.equal(
+    JSON.parse(fs.readFileSync(path.join(worktreeCwd, ".paperclip", "seed-manifest.json"), "utf8")).state,
+    "verified",
+  );
+});
+
 test("runtime provisioning leaves seed-pending in place when ensure-seeded fails", () => {
   const baseCwd = makeBaseWorkspace({ helpExit: 0, initExit: 0, ensureExit: 4 });
   const worktreeCwd = makeTempDir("paperclip-provision-runtime-failure-");