[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>

packages/adapter-utils/src/server-utils.ts

@@ -1,6 +1,7 @@
 import { spawn, type ChildProcess } from "node:child_process";
 import { createHash, randomUUID } from "node:crypto";
 import { constants as fsConstants, promises as fs, type Dirent } from "node:fs";
+import os from "node:os";
 import path from "node:path";
 import { sanitizeRemoteExecutionEnv } from "./remote-execution-env.js";
 import { buildSshSpawnTarget, type SshRemoteExecutionSpec } from "./ssh.js";
@@ -78,6 +79,8 @@ export const runningProcesses = new Map<string, RunningProcess>();
 export const MAX_CAPTURE_BYTES = 4 * 1024 * 1024;
 export const MAX_EXCERPT_BYTES = 32 * 1024;
 const TERMINAL_RESULT_SCAN_OVERLAP_CHARS = 64 * 1024;
+const DEFAULT_PAPERCLIP_INSTANCE_ID = "default";
+const PATH_SEGMENT_RE = /^[a-zA-Z0-9_-]+$/;
 const SENSITIVE_ENV_KEY = /(key|token|secret|password|passwd|authorization|cookie)/i;
 const REDACTED_LOG_VALUE = "***REDACTED***";
 const PAPERCLIP_SKILL_ROOT_RELATIVE_CANDIDATES = [
@@ -88,6 +91,25 @@ const MATERIALIZED_SKILL_SENTINEL = ".paperclip-materialized-skill.json";
 const MATERIALIZED_SKILL_LOCK_OWNER = "owner.json";
 const MATERIALIZED_SKILL_LOCK_STALE_MS = 30_000;
 
+function expandHomePrefix(value: string): string {
+  if (value === "~") return os.homedir();
+  if (value.startsWith("~/")) return path.resolve(os.homedir(), value.slice(2));
+  return value;
+}
+
+export function resolvePaperclipInstanceRootForAdapter(input: {
+  homeDir?: string;
+  instanceId?: string;
+  env?: NodeJS.ProcessEnv;
+} = {}): string {
+  const env = input.env ?? process.env;
+  const homeRaw = input.homeDir?.trim() || env.PAPERCLIP_HOME?.trim();
+  const homeDir = path.resolve(homeRaw ? expandHomePrefix(homeRaw) : path.resolve(os.homedir(), ".paperclip"));
+  const instanceId = input.instanceId?.trim() || env.PAPERCLIP_INSTANCE_ID?.trim() || DEFAULT_PAPERCLIP_INSTANCE_ID;
+  if (!PATH_SEGMENT_RE.test(instanceId)) throw new Error(`Invalid PAPERCLIP_INSTANCE_ID '${instanceId}'.`);
+  return path.resolve(homeDir, "instances", instanceId);
+}
+
 export const DEFAULT_PAPERCLIP_AGENT_PROMPT_TEMPLATE = [
   "You are agent {{agent.id}} ({{agent.name}}). Continue your Paperclip work.",
   "",