[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>

server/src/services/plugin-host-services.ts

@@ -44,10 +44,12 @@ import { pluginStateStore } from "./plugin-state-store.js";
 import { pluginDatabaseService } from "./plugin-database.js";
 import { pluginManagedAgentService } from "./plugin-managed-agents.js";
 import { pluginManagedRoutineService } from "./plugin-managed-routines.js";
+import { pluginManagedSkillService } from "./plugin-managed-skills.js";
 import {
   assertConfiguredLocalFolder,
   assertWritableConfiguredLocalFolder,
   getStoredLocalFolders,
+  deletePluginLocalFolderFile,
   inspectPluginLocalFolder,
   listPluginLocalFolderEntries,
   preparePluginLocalFolder,
@@ -509,6 +511,11 @@ export function buildHostServices(
     manifest: options.manifest,
     pluginWorkerManager: options.pluginWorkerManager,
   });
+  const managedSkills = pluginManagedSkillService(db, {
+    pluginId,
+    pluginKey,
+    manifest: options.manifest,
+  });
   const heartbeat = heartbeatService(db, {
     pluginWorkerManager: options.pluginWorkerManager,
   });
@@ -882,12 +889,17 @@ export function buildHostServices(
         });
         const status = await inspectStoredLocalFolder(companyId, params.folderKey);
         assertWritableConfiguredLocalFolder(status);
-        if (status.access !== "readWrite" || !status.writable) {
-          throw new Error("Local folder is not configured for writes");
-        }
         await writePluginLocalFolderTextAtomic(status.realPath!, params.relativePath, params.contents);
         return inspectStoredLocalFolder(companyId, params.folderKey);
       },
+
+      async deleteFile(params) {
+        const companyId = ensureCompanyId(params.companyId);
+        const status = await inspectStoredLocalFolder(companyId, params.folderKey);
+        assertWritableConfiguredLocalFolder(status);
+        await deletePluginLocalFolderFile(status.realPath!, params.relativePath, params.folderKey);
+        return inspectStoredLocalFolder(companyId, params.folderKey);
+      },
     },
 
     state: {
@@ -1224,6 +1236,24 @@ export function buildHostServices(
       },
     },
 
+    skills: {
+      async managedGet(params) {
+        const companyId = ensureCompanyId(params.companyId);
+        await ensurePluginAvailableForCompany(companyId);
+        return managedSkills.get(params.skillKey, companyId);
+      },
+      async managedReconcile(params) {
+        const companyId = ensureCompanyId(params.companyId);
+        await ensurePluginAvailableForCompany(companyId);
+        return managedSkills.reconcile(params.skillKey, companyId);
+      },
+      async managedReset(params) {
+        const companyId = ensureCompanyId(params.companyId);
+        await ensurePluginAvailableForCompany(companyId);
+        return managedSkills.reset(params.skillKey, companyId);
+      },
+    },
+
     issues: {
       async list(params) {
         const companyId = ensureCompanyId(params.companyId);