Fix LLM Wiki package and migration validation (#6010)

## Thinking Path

> - Paperclip orchestrates AI agents for zero-human companies.
> - Plugins extend the control plane with optional capabilities such as
LLM Wiki.
> - LLM Wiki needs its package assets and plugin-owned database
migrations to work when installed from the packaged plugin.
> - The bundled spaces migration used validation-hostile dynamic SQL,
and the packaged plugin could omit non-dist runtime assets.
> - This pull request makes the LLM Wiki package include its required
assets and cuts the spaces migration over to explicit, idempotent SQL
that passes the production plugin database validator.
> - The benefit is a simpler plugin install path that validates and
applies the bundled LLM Wiki migrations without adding plugin-specific
legacy handling to Paperclip core.

## What Changed

- Added the LLM Wiki package asset allowlist so agents, migrations,
skills, templates, dist output, and README are included when packaged.
- Renamed the bootstrap `.gitignore` template to `gitignore.template`
and updated the runtime lookup so package tooling does not drop the
hidden template file.
- Relaxed plugin migration validation to allow namespace-scoped
`INSERT`/`UPDATE` backfills and `CREATE INDEX` statements while
continuing to reject destructive or cross-namespace SQL.
- Replaced the LLM Wiki spaces migration's dynamic constraint-drop DO
block with explicit `DROP CONSTRAINT IF EXISTS` statements.
- Replaced fragile regex-source dispatch in SQL reference extraction
with explicit capture-group descriptors.
- Added regression coverage that applies the bundled LLM Wiki migrations
through the production validator and checks the expected constraints.

## Verification

- `pnpm exec vitest run --project @paperclipai/server
server/src/__tests__/plugin-database.test.ts --pool=forks
--poolOptions.forks.isolate=true`
- `pnpm --filter @paperclipai/plugin-llm-wiki build`
- `git diff --check`
- Confirmed `pnpm-lock.yaml` is not included in the branch diff.

## Risks

- Low migration risk for current users: LLM Wiki spaces are new, so this
intentionally cuts over the plugin migration instead of adding legacy
handling in core.
- Validator behavior is broader than before, but still requires fully
qualified plugin namespace targets, blocks deletes/destructive DDL, and
keeps public table access read-only and allowlisted.

> Checked [`ROADMAP.md`](ROADMAP.md); this is a targeted plugin
packaging/migration fix and does not duplicate planned core feature
work. See `CONTRIBUTING.md`.

## Model Used

- OpenAI Codex, GPT-5 based coding agent, tool-enabled local repo
access, reasoning mode managed by the Paperclip/Codex runtime. Exact
context window was not surfaced in this session.

## 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
- [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

---------

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

packages/plugins/plugin-llm-wiki/migrations/003_spaces.sql

@@ -140,37 +140,14 @@ ALTER TABLE plugin_llm_wiki_8f50da974f.paperclip_distillation_runs ALTER COLUMN
 ALTER TABLE plugin_llm_wiki_8f50da974f.paperclip_source_snapshots ALTER COLUMN space_id SET NOT NULL;
 ALTER TABLE plugin_llm_wiki_8f50da974f.paperclip_page_bindings ALTER COLUMN space_id SET NOT NULL;
 
-DO $$
-DECLARE
-  target record;
-  constraint_name text;
-BEGIN
-  FOR target IN
-    SELECT * FROM (VALUES
-      ('wiki_pages', ARRAY['company_id', 'wiki_id', 'path']::text[]),
-      ('paperclip_distillation_cursors', ARRAY['company_id', 'wiki_id', 'source_scope', 'scope_key', 'source_kind']::text[]),
-      ('paperclip_distillation_work_items', ARRAY['company_id', 'wiki_id', 'idempotency_key']::text[]),
-      ('paperclip_page_bindings', ARRAY['company_id', 'wiki_id', 'page_path']::text[])
-    ) AS targets(table_name, column_names)
-  LOOP
-    FOR constraint_name IN
-      SELECT c.conname
-      FROM pg_constraint c
-      JOIN pg_class t ON t.oid = c.conrelid
-      JOIN pg_namespace n ON n.oid = t.relnamespace
-      WHERE n.nspname = 'plugin_llm_wiki_8f50da974f'
-        AND t.relname = target.table_name
-        AND c.contype = 'u'
-        AND (
-          SELECT array_agg(a.attname ORDER BY constraint_columns.ordinality)::text[]
-          FROM unnest(c.conkey) WITH ORDINALITY AS constraint_columns(attnum, ordinality)
-          JOIN pg_attribute a ON a.attrelid = c.conrelid AND a.attnum = constraint_columns.attnum
-        ) = target.column_names
-    LOOP
-      EXECUTE format('ALTER TABLE %I.%I DROP CONSTRAINT %I', 'plugin_llm_wiki_8f50da974f', target.table_name, constraint_name);
-    END LOOP;
-  END LOOP;
-END $$;
+ALTER TABLE plugin_llm_wiki_8f50da974f.wiki_pages
+  DROP CONSTRAINT IF EXISTS wiki_pages_company_id_wiki_id_path_key;
+ALTER TABLE plugin_llm_wiki_8f50da974f.paperclip_distillation_cursors
+  DROP CONSTRAINT IF EXISTS paperclip_distillation_cursor_company_id_wiki_id_source_sco_key;
+ALTER TABLE plugin_llm_wiki_8f50da974f.paperclip_distillation_work_items
+  DROP CONSTRAINT IF EXISTS paperclip_distillation_work_i_company_id_wiki_id_idempotenc_key;
+ALTER TABLE plugin_llm_wiki_8f50da974f.paperclip_page_bindings
+  DROP CONSTRAINT IF EXISTS paperclip_page_bindings_company_id_wiki_id_page_path_key;
 
 ALTER TABLE plugin_llm_wiki_8f50da974f.wiki_pages
   DROP CONSTRAINT IF EXISTS wiki_pages_company_wiki_space_path_key;

packages/plugins/plugin-llm-wiki/package.json

@@ -4,6 +4,14 @@
   "type": "module",
   "private": true,
   "description": "Local-file LLM Wiki plugin for source ingestion, wiki browsing, query, lint, and maintenance workflows.",
+  "files": [
+    "agents",
+    "dist",
+    "migrations",
+    "skills",
+    "templates",
+    "README.md"
+  ],
   "scripts": {
     "prebuild": "pnpm --filter @paperclipai/plugin-sdk ensure-build-deps",
     "build": "node ./esbuild.config.mjs",

packages/plugins/plugin-llm-wiki/src/templates.ts

@@ -46,7 +46,7 @@ export const DEFAULT_AGENT_INSTRUCTIONS = DEFAULT_AGENT_INSTRUCTION_FILES["AGENT
 export const DEFAULT_IDEA = templateFile("IDEA.md");
 export const DEFAULT_INDEX = templateFile("wiki/index.md");
 export const DEFAULT_LOG = templateFile("wiki/log.md");
-export const DEFAULT_GITIGNORE = templateFile(".gitignore");
+export const DEFAULT_GITIGNORE = templateFile("gitignore.template");
 
 export const QUERY_PROMPT = `Answer from the LLM Wiki using the installed wiki-query skill.