[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/shared/src/validators/plugin.test.ts

@@ -1,6 +1,6 @@
 import { describe, expect, it } from "vitest";
 import { PLUGIN_CAPABILITIES } from "../constants.js";
-import { pluginManagedRoutineDeclarationSchema, pluginUiSlotDeclarationSchema } from "./plugin.js";
+import { pluginManagedRoutineDeclarationSchema, pluginManifestV1Schema, pluginUiSlotDeclarationSchema } from "./plugin.js";
 
 describe("plugin capability constants", () => {
   it("exposes each capability once", () => {
@@ -30,6 +30,41 @@ describe("plugin managed routine validators", () => {
   });
 });
 
+describe("plugin managed skill validators", () => {
+  const baseManifest = {
+    id: "paperclip.test-managed-skills",
+    apiVersion: 1,
+    version: "0.1.0",
+    displayName: "Managed Skills",
+    description: "Managed skills test plugin.",
+    author: "Paperclip",
+    categories: ["automation"],
+    entrypoints: { worker: "./dist/worker.js" },
+  } as const;
+
+  it("requires skills.managed when managed skills are declared", () => {
+    const parsed = pluginManifestV1Schema.safeParse({
+      ...baseManifest,
+      capabilities: [],
+      skills: [{ skillKey: "wiki-maintainer", displayName: "Wiki Maintainer" }],
+    });
+
+    expect(parsed.success).toBe(false);
+    if (parsed.success) return;
+    expect(parsed.error.issues.some((issue) => issue.message.includes("skills.managed"))).toBe(true);
+  });
+
+  it("accepts managed skills with the skills.managed capability", () => {
+    const parsed = pluginManifestV1Schema.parse({
+      ...baseManifest,
+      capabilities: ["skills.managed"],
+      skills: [{ skillKey: "wiki-maintainer", displayName: "Wiki Maintainer" }],
+    });
+
+    expect(parsed.skills?.[0]?.skillKey).toBe("wiki-maintainer");
+  });
+});
+
 describe("plugin UI slot validators", () => {
   it("accepts route-scoped sidebar slots with a routePath", () => {
     const parsed = pluginUiSlotDeclarationSchema.parse({