[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/adapters/acpx-local/src/server/execute.ts

@@ -21,6 +21,7 @@ import {
   readPaperclipIssueWorkModeFromContext,
   renderPaperclipWakePrompt,
   renderTemplate,
+  resolvePaperclipInstanceRootForAdapter,
   resolvePaperclipDesiredSkillNames,
   rewriteWorkspaceCwdEnvVarsForExecution,
   shapePaperclipWorkspaceEnvForExecution,
@@ -115,7 +116,10 @@ function shortHash(value: unknown): string {
 function defaultPaperclipInstanceDir(): string {
   const home = process.env.PAPERCLIP_HOME?.trim() || path.join(os.homedir(), ".paperclip");
   const instanceId = process.env.PAPERCLIP_INSTANCE_ID?.trim() || "default";
-  return path.join(home, "instances", instanceId);
+  return resolvePaperclipInstanceRootForAdapter({
+    homeDir: home,
+    instanceId,
+  });
 }
 
 function defaultStateDir(companyId: string, agentId: string): string {

packages/adapters/claude-local/src/server/claude-config.ts

@@ -3,8 +3,8 @@ import fs from "node:fs/promises";
 import os from "node:os";
 import path from "node:path";
 import type { AdapterExecutionContext } from "@paperclipai/adapter-utils";
+import { resolvePaperclipInstanceRootForAdapter } from "@paperclipai/adapter-utils/server-utils";
 
-const DEFAULT_PAPERCLIP_INSTANCE_ID = "default";
 const SEEDED_SHARED_FILES = [
   ".credentials.json",
   "credentials.json",
@@ -92,11 +92,14 @@ export function resolveManagedClaudeConfigSeedDir(
   env: NodeJS.ProcessEnv,
   companyId?: string,
 ): string {
-  const paperclipHome = nonEmpty(env.PAPERCLIP_HOME) ?? path.resolve(os.homedir(), ".paperclip");
-  const instanceId = nonEmpty(env.PAPERCLIP_INSTANCE_ID) ?? DEFAULT_PAPERCLIP_INSTANCE_ID;
+  const instanceRoot = resolvePaperclipInstanceRootForAdapter({
+    homeDir: nonEmpty(env.PAPERCLIP_HOME) ?? undefined,
+    instanceId: nonEmpty(env.PAPERCLIP_INSTANCE_ID) ?? undefined,
+    env,
+  });
   return companyId
-    ? path.resolve(paperclipHome, "instances", instanceId, "companies", companyId, "claude-config-seed")
-    : path.resolve(paperclipHome, "instances", instanceId, "claude-config-seed");
+    ? path.resolve(instanceRoot, "companies", companyId, "claude-config-seed")
+    : path.resolve(instanceRoot, "claude-config-seed");
 }
 
 export async function prepareClaudeConfigSeed(

packages/adapters/claude-local/src/server/prompt-cache.ts

@@ -1,12 +1,13 @@
 import { constants as fsConstants } from "node:fs";
 import fs from "node:fs/promises";
-import os from "node:os";
 import path from "node:path";
 import { createHash, type Hash } from "node:crypto";
 import type { AdapterExecutionContext } from "@paperclipai/adapter-utils";
-import { ensurePaperclipSkillSymlink, type PaperclipSkillEntry } from "@paperclipai/adapter-utils/server-utils";
-
-const DEFAULT_PAPERCLIP_INSTANCE_ID = "default";
+import {
+  ensurePaperclipSkillSymlink,
+  resolvePaperclipInstanceRootForAdapter,
+  type PaperclipSkillEntry,
+} from "@paperclipai/adapter-utils/server-utils";
 
 type SkillEntry = PaperclipSkillEntry;
 
@@ -25,12 +26,13 @@ function resolveManagedClaudePromptCacheRoot(
   env: NodeJS.ProcessEnv,
   companyId: string,
 ): string {
-  const paperclipHome = nonEmpty(env.PAPERCLIP_HOME) ?? path.resolve(os.homedir(), ".paperclip");
-  const instanceId = nonEmpty(env.PAPERCLIP_INSTANCE_ID) ?? DEFAULT_PAPERCLIP_INSTANCE_ID;
+  const instanceRoot = resolvePaperclipInstanceRootForAdapter({
+    homeDir: nonEmpty(env.PAPERCLIP_HOME) ?? undefined,
+    instanceId: nonEmpty(env.PAPERCLIP_INSTANCE_ID) ?? undefined,
+    env,
+  });
   return path.resolve(
-    paperclipHome,
-    "instances",
-    instanceId,
+    instanceRoot,
     "companies",
     companyId,
     "claude-prompt-cache",

packages/adapters/codex-local/src/server/codex-home.ts

@@ -2,11 +2,11 @@ import fs from "node:fs/promises";
 import os from "node:os";
 import path from "node:path";
 import type { AdapterExecutionContext } from "@paperclipai/adapter-utils";
+import { resolvePaperclipInstanceRootForAdapter } from "@paperclipai/adapter-utils/server-utils";
 
 const TRUTHY_ENV_RE = /^(1|true|yes|on)$/i;
 const COPIED_SHARED_FILES = ["config.json", "config.toml", "instructions.md"] as const;
 const SYMLINKED_SHARED_FILES = ["auth.json"] as const;
-const DEFAULT_PAPERCLIP_INSTANCE_ID = "default";
 
 function nonEmpty(value: string | undefined): string | null {
   return typeof value === "string" && value.trim().length > 0 ? value.trim() : null;
@@ -31,11 +31,14 @@ export function resolveManagedCodexHomeDir(
   env: NodeJS.ProcessEnv,
   companyId?: string,
 ): string {
-  const paperclipHome = nonEmpty(env.PAPERCLIP_HOME) ?? path.resolve(os.homedir(), ".paperclip");
-  const instanceId = nonEmpty(env.PAPERCLIP_INSTANCE_ID) ?? DEFAULT_PAPERCLIP_INSTANCE_ID;
+  const instanceRoot = resolvePaperclipInstanceRootForAdapter({
+    homeDir: nonEmpty(env.PAPERCLIP_HOME) ?? undefined,
+    instanceId: nonEmpty(env.PAPERCLIP_INSTANCE_ID) ?? undefined,
+    env,
+  });
   return companyId
-    ? path.resolve(paperclipHome, "instances", instanceId, "companies", companyId, "codex-home")
-    : path.resolve(paperclipHome, "instances", instanceId, "codex-home");
+    ? path.resolve(instanceRoot, "companies", companyId, "codex-home")
+    : path.resolve(instanceRoot, "codex-home");
 }
 
 async function ensureParentDir(target: string): Promise<void> {