[codex] Add LLM Wiki plugin host support (#5597)

## Thinking Path

> - Paperclip orchestrates AI agents for zero-human companies.
> - The plugin system needs host contracts and runtime support before
large plugins can integrate cleanly.
> - The source branch mixed the LLM Wiki package with supporting
host/runtime work, managed plugin skills, root-level storage spaces, and
a bookmarks reference plugin.
> - [PAP-9173](/PAP/issues/PAP-9173) asked for the current branch to be
split by file boundary: plugin package separately from everything else.
> - [PAP-9188](/PAP/issues/PAP-9188) clarified that LLM Wiki may have
plugin-local spaces, but Paperclip core should not reorganize top-level
local storage into spaces.
> - Follow-up review clarified that the bookmarks example should not
ship in this PR either.
> - This pull request contains the
non-`packages/plugins/plugin-llm-wiki/` host/runtime work, keeps runtime
state under the selected Paperclip instance root, and no longer includes
the bookmarks example.

## What Changed

- Added/updated plugin host contracts, SDK types, worker RPC plumbing,
managed plugin skill support, and related server tests.
- Removed the bookmarks example plugin package and its
bundled-example/workspace references.
- Removed the root-level local spaces CLI/migration surface and restored
instance-root runtime defaults for config, db, logs, storage, secrets,
workspaces, projects, and adapter homes.
- Replaced shared root `space-paths` helpers with `home-paths` helpers
for core runtime storage.
- Tightened stranded recovery unique-conflict detection so concurrent
recovery scans reuse the raced recovery issue when Postgres errors are
wrapped.
- Kept `packages/plugins/plugin-llm-wiki/` out of this PR diff;
plugin-local spaces remain in the stacked plugin-only PR.

## Verification

- `pnpm exec vitest run cli/src/__tests__/data-dir.test.ts
cli/src/__tests__/home-paths.test.ts cli/src/__tests__/onboard.test.ts
packages/shared/src/home-paths.test.ts
packages/db/src/runtime-config.test.ts
server/src/__tests__/agent-instructions-service.test.ts
server/src/__tests__/claude-local-execute.test.ts
server/src/__tests__/codex-local-execute.test.ts`
- `pnpm exec vitest run packages/db/src/runtime-config.test.ts`
- `pnpm exec vitest run
server/src/__tests__/plugin-routes-authz.test.ts`
- `pnpm --filter @paperclipai/server typecheck`
- `pnpm exec vitest run
server/src/__tests__/heartbeat-process-recovery.test.ts -t "reuses the
raced stranded recovery issue"` skipped locally because embedded
Postgres did not initialize on this macOS temp host; the code path was
typechecked and is covered by Linux CI.
- Boundary check: no core references remain for `PAPERCLIP_SPACE_ID`,
`spaces migrate-default`, `@paperclipai/shared/space-paths`,
`registerSpacesCommands`, or the removed bookmarks example.
- Previous PR head `4f23e034` had green GitHub checks: `verify`, all
four serialized server shards, `e2e`, `Canary Dry Run`, `policy`, Snyk,
and `Greptile Review`. Current head `582f466d` is re-running checks
after the bookmarks deletion.

## Risks

- Plugin host changes touch shared runtime paths, so regressions would
most likely appear in adapter startup, plugin loading, or local dev path
defaults.
- Removing the bookmarks example also removes one demonstration of
plugin database namespaces plus local-folder persistence; remaining
plugin examples still cover bundled example discovery and plugin host
flows.
- The plugin package itself is intentionally deferred to the stacked
plugin-only PR, where LLM Wiki plugin-local spaces live.
- Existing installs that tested the transient root-level spaces CLI
should stop using it; this PR intentionally removes that unsupported
migration surface before merge.

> 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 GPT-5 Codex via Codex CLI, tool use and local code execution
enabled; context window not exposed.

## 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 run tests locally and they pass, except where noted above
for host-specific embedded Postgres initialization
- [x] I have added or updated tests where applicable
- [x] If this change affects the UI, I have included before/after
screenshots
- [x] I have updated relevant documentation to reflect my changes
- [x] I have considered and documented any risks above
- [x] I will address all Greptile and reviewer comments before
requesting merge

Stacked follow-up: PR #5592 contains only
`packages/plugins/plugin-llm-wiki/` and targets this branch.

---------

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

cli/src/__tests__/home-paths.test.ts

@@ -1,3 +1,4 @@
+import fs from "node:fs";
 import os from "node:os";
 import path from "node:path";
 import { afterEach, describe, expect, it } from "vitest";
@@ -16,13 +17,14 @@ describe("home path resolution", () => {
   });
 
   it("defaults to ~/.paperclip and default instance", () => {
-    delete process.env.PAPERCLIP_HOME;
+    const home = fs.mkdtempSync(path.join(os.tmpdir(), "paperclip-home-paths-"));
+    process.env.PAPERCLIP_HOME = home;
     delete process.env.PAPERCLIP_INSTANCE_ID;
 
     const paths = describeLocalInstancePaths();
-    expect(paths.homeDir).toBe(path.resolve(os.homedir(), ".paperclip"));
+    expect(paths.homeDir).toBe(home);
     expect(paths.instanceId).toBe("default");
-    expect(paths.configPath).toBe(path.resolve(os.homedir(), ".paperclip", "instances", "default", "config.json"));
+    expect(paths.configPath).toBe(path.resolve(home, "instances", "default", "config.json"));
   });
 
   it("supports PAPERCLIP_HOME and explicit instance ids", () => {
@@ -34,7 +36,7 @@ describe("home path resolution", () => {
   });
 
   it("rejects invalid instance ids", () => {
-    expect(() => resolvePaperclipInstanceId("bad/id")).toThrow(/Invalid instance id/);
+    expect(() => resolvePaperclipInstanceId("bad/id")).toThrow(/Invalid PAPERCLIP_INSTANCE_ID/);
   });
 
   it("expands ~ prefixes", () => {

cli/src/__tests__/onboard.test.ts

@@ -6,6 +6,7 @@ import { onboard } from "../commands/onboard.js";
 import type { PaperclipConfig } from "../config/schema.js";
 
 const ORIGINAL_ENV = { ...process.env };
+const ORIGINAL_CWD = process.cwd();
 
 function createExistingConfigFixture() {
   const root = fs.mkdtempSync(path.join(os.tmpdir(), "paperclip-onboard-"));
@@ -85,10 +86,18 @@ describe("onboard", () => {
     delete process.env.PAPERCLIP_AGENT_JWT_SECRET;
     delete process.env.PAPERCLIP_SECRETS_MASTER_KEY;
     delete process.env.PAPERCLIP_SECRETS_MASTER_KEY_FILE;
+    delete process.env.PAPERCLIP_HOME;
+    delete process.env.PAPERCLIP_CONFIG;
+    delete process.env.PAPERCLIP_INSTANCE_ID;
+    delete process.env.PAPERCLIP_BIND;
+    delete process.env.PAPERCLIP_BIND_HOST;
+    delete process.env.PAPERCLIP_TAILNET_BIND_HOST;
+    delete process.env.HOST;
   });
 
   afterEach(() => {
     process.env = { ...ORIGINAL_ENV };
+    process.chdir(ORIGINAL_CWD);
   });
 
   it("preserves an existing config when rerun without flags", async () => {
@@ -125,6 +134,27 @@ describe("onboard", () => {
     expect(raw.server.host).toBe("127.0.0.1");
   });
 
+  it("creates instance-root config and data paths for a fresh PAPERCLIP_HOME", async () => {
+    const home = fs.mkdtempSync(path.join(os.tmpdir(), "paperclip-onboard-home-"));
+    const cwd = fs.mkdtempSync(path.join(os.tmpdir(), "paperclip-onboard-cwd-"));
+    process.chdir(cwd);
+    process.env.PAPERCLIP_HOME = home;
+
+    await onboard({ yes: true, invokedByRun: true });
+
+    const instanceRoot = path.join(home, "instances", "default");
+    const configPath = path.join(instanceRoot, "config.json");
+    const raw = JSON.parse(fs.readFileSync(configPath, "utf8")) as PaperclipConfig;
+
+    expect(raw.database.embeddedPostgresDataDir).toBe(path.join(instanceRoot, "db"));
+    expect(raw.database.backup.dir).toBe(path.join(instanceRoot, "data", "backups"));
+    expect(raw.logging.logDir).toBe(path.join(instanceRoot, "logs"));
+    expect(raw.storage.localDisk.baseDir).toBe(path.join(instanceRoot, "data", "storage"));
+    expect(raw.secrets.localEncrypted.keyFilePath).toBe(path.join(instanceRoot, "secrets", "master.key"));
+    expect(fs.existsSync(path.join(instanceRoot, ".env"))).toBe(true);
+    expect(fs.existsSync(path.join(instanceRoot, "secrets", "master.key"))).toBe(true);
+  });
+
   it("supports authenticated/private quickstart bind presets", async () => {
     const configPath = createFreshConfigPath();
     process.env.PAPERCLIP_TAILNET_BIND_HOST = "100.64.0.8";

cli/src/config/home.ts

@@ -1,32 +1,31 @@
-import os from "node:os";
 import path from "node:path";
+import {
+  expandHomePrefix,
+  resolveDefaultBackupDir as resolveSharedDefaultBackupDir,
+  resolveDefaultEmbeddedPostgresDir as resolveSharedDefaultEmbeddedPostgresDir,
+  resolveDefaultLogsDir as resolveSharedDefaultLogsDir,
+  resolveDefaultSecretsKeyFilePath as resolveSharedDefaultSecretsKeyFilePath,
+  resolveDefaultStorageDir as resolveSharedDefaultStorageDir,
+  resolveHomeAwarePath,
+  resolvePaperclipConfigPathForInstance,
+  resolvePaperclipHomeDir,
+  resolvePaperclipInstanceId,
+  resolvePaperclipInstanceRoot as resolveSharedPaperclipInstanceRoot,
+} from "@paperclipai/shared/home-paths";
 
-const DEFAULT_INSTANCE_ID = "default";
-const INSTANCE_ID_RE = /^[a-zA-Z0-9_-]+$/;
-
-export function resolvePaperclipHomeDir(): string {
-  const envHome = process.env.PAPERCLIP_HOME?.trim();
-  if (envHome) return path.resolve(expandHomePrefix(envHome));
-  return path.resolve(os.homedir(), ".paperclip");
-}
-
-export function resolvePaperclipInstanceId(override?: string): string {
-  const raw = override?.trim() || process.env.PAPERCLIP_INSTANCE_ID?.trim() || DEFAULT_INSTANCE_ID;
-  if (!INSTANCE_ID_RE.test(raw)) {
-    throw new Error(
-      `Invalid instance id '${raw}'. Allowed characters: letters, numbers, '_' and '-'.`,
-    );
-  }
-  return raw;
-}
+export {
+  expandHomePrefix,
+  resolveHomeAwarePath,
+  resolvePaperclipHomeDir,
+  resolvePaperclipInstanceId,
+};
 
 export function resolvePaperclipInstanceRoot(instanceId?: string): string {
-  const id = resolvePaperclipInstanceId(instanceId);
-  return path.resolve(resolvePaperclipHomeDir(), "instances", id);
+  return resolveSharedPaperclipInstanceRoot({ instanceId });
 }
 
 export function resolveDefaultConfigPath(instanceId?: string): string {
-  return path.resolve(resolvePaperclipInstanceRoot(instanceId), "config.json");
+  return resolvePaperclipConfigPathForInstance({ instanceId });
 }
 
 export function resolveDefaultContextPath(): string {
@@ -38,29 +37,23 @@ export function resolveDefaultCliAuthPath(): string {
 }
 
 export function resolveDefaultEmbeddedPostgresDir(instanceId?: string): string {
-  return path.resolve(resolvePaperclipInstanceRoot(instanceId), "db");
+  return resolveSharedDefaultEmbeddedPostgresDir({ instanceId });
 }
 
 export function resolveDefaultLogsDir(instanceId?: string): string {
-  return path.resolve(resolvePaperclipInstanceRoot(instanceId), "logs");
+  return resolveSharedDefaultLogsDir({ instanceId });
 }
 
 export function resolveDefaultSecretsKeyFilePath(instanceId?: string): string {
-  return path.resolve(resolvePaperclipInstanceRoot(instanceId), "secrets", "master.key");
+  return resolveSharedDefaultSecretsKeyFilePath({ instanceId });
 }
 
 export function resolveDefaultStorageDir(instanceId?: string): string {
-  return path.resolve(resolvePaperclipInstanceRoot(instanceId), "data", "storage");
+  return resolveSharedDefaultStorageDir({ instanceId });
 }
 
 export function resolveDefaultBackupDir(instanceId?: string): string {
-  return path.resolve(resolvePaperclipInstanceRoot(instanceId), "data", "backups");
-}
-
-export function expandHomePrefix(value: string): string {
-  if (value === "~") return os.homedir();
-  if (value.startsWith("~/")) return path.resolve(os.homedir(), value.slice(2));
-  return value;
+  return resolveSharedDefaultBackupDir({ instanceId });
 }
 
 export function describeLocalInstancePaths(instanceId?: string) {