docs: update tools, sync, and CI documentation

* ci: add workflow to sync OSA submodule via auto-PR

Receives repository_dispatch from the OSA repo on push to main,
updates the submodule ref, and opens/updates a PR. Includes weekly
scheduled fallback.

* docs: add BIDS and EEGLAB tool pages, rewrite tools overview and HED docs

- Create tools/bids.md documenting all BIDS tools including lookup_bep
- Create tools/eeglab.md documenting docstring search, FAQ search, and
  knowledge tools
- Rewrite tools/index.md to reflect multi-community architecture with
  community-scoped tool naming pattern
- Fix tools/hed.md: add missing knowledge tools, fix return value types
- Add new tool pages to mkdocs.yml navigation

* docs: rewrite knowledge-sync.md for multi-community architecture

- Add --community/-c flag to all sync commands
- Document new sync types: docstrings, mailman, faq, beps
- Fix automated sync section: schedules are per-community YAML config,
  not environment variables
- Update agent tools section with community-scoped names
- Fix troubleshooting: remove incorrect gh CLI requirement
- Update database location to {community_id}.db pattern

* docs: update CLI reference, schema, and registry pages

- cli-reference: add new sync subcommands, fix env var table
- schema-reference: add mailman, docstrings, faq_generation, sync,
  budget, and maintainers config sections
- registry/index: show BIDS and EEGLAB as implemented
- extensions: fix tool loading order, add docstring/FAQ tools
- quick-start, local-testing: fix incorrect --citations flag usage

* docs: fix review findings in tool and sync pages

Fix doc counts (BIDS: 49->46, EEGLAB: 22->25), add missing setup
category to EEGLAB on-demand docs breakdown, and expand abbreviations
on first use (FTS5, PR, ICA, FAQ, LLM, LSL) across tool and sync pages.

Author: neuromechanist

.github/workflows/sync-osa-submodule.yml

@@ -0,0 +1,40 @@
+name: Sync OSA Submodule
+
+on:
+  repository_dispatch:
+    types: [osa-updated]
+  schedule:
+    - cron: "0 6 * * 1"  # Weekly Monday 6am UTC as fallback
+  workflow_dispatch:
+
+jobs:
+  sync:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+      pull-requests: write
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          submodules: true
+          fetch-depth: 0
+
+      - name: Update OSA submodule
+        run: |
+          git submodule update --remote osa
+          echo "Updated OSA submodule to $(git -C osa rev-parse --short HEAD)"
+
+      - name: Create Pull Request
+        uses: peter-evans/create-pull-request@v7
+        with:
+          commit-message: "sync: update OSA submodule to latest"
+          title: "sync: update OSA submodule to latest"
+          body: |
+            Automated update of the OSA submodule to track latest changes.
+
+            Triggered by: ${{ github.event_name }}
+          branch: sync/osa-submodule
+          labels: sync
+          delete-branch: true

docs/osa/cli-reference.md

@@ -201,24 +201,40 @@ Options:
 
 ### `osa sync`
 
-Sync knowledge sources (GitHub issues/PRs, academic papers). Requires server dependencies.
-See [Knowledge Sync](knowledge-sync.md) for details.
+Sync knowledge sources for community assistants. Requires server dependencies. All subcommands accept `--community/-c` to specify the target community.
+
+See [Knowledge Sync](knowledge-sync.md) for full documentation.
 
 ```bash
-# Initialize database
-osa sync init
+# Initialize database for a community
+osa sync init --community hed
 
 # Sync GitHub issues/PRs
-osa sync github
+osa sync github --community bids
+
+# Sync academic papers (with citation tracking)
+osa sync papers --community bids
+
+# Sync code docstrings (MATLAB/Python)
+osa sync docstrings --community eeglab --language matlab
+
+# Sync mailing list archives
+osa sync mailman --community eeglab
 
-# Sync academic papers
-osa sync papers
+# Generate FAQ from mailing list threads
+osa sync faq --community eeglab --estimate
 
-# Sync everything
+# Sync BIDS Extension Proposals
+osa sync beps --community bids
+
+# Sync everything for all communities
 osa sync all
 
 # Check status
 osa sync status
+
+# Search knowledge database
+osa sync search "validation error" --community hed
 ```
 
 ## Configuration
@@ -273,11 +289,15 @@ These are only relevant when running the server (`osa serve`):
 | `LANGFUSE_PUBLIC_KEY` | LangFuse public key | Optional |
 | `LANGFUSE_SECRET_KEY` | LangFuse secret key | Optional |
 | `SYNC_ENABLED` | Enable automated knowledge sync | `true` |
-| `SYNC_GITHUB_CRON` | GitHub sync schedule (cron) | `0 2 * * *` |
-| `SYNC_PAPERS_CRON` | Papers sync schedule (cron) | `0 3 * * 0` |
-| `GITHUB_TOKEN` | GitHub token for sync | Optional |
+| `GITHUB_TOKEN` | GitHub token for sync (higher rate limits) | Optional |
+| `SEMANTIC_SCHOLAR_API_KEY` | Semantic Scholar API key | Optional |
+| `PUBMED_API_KEY` | PubMed/NCBI API key | Optional |
+| `OPENALEX_EMAIL` | Email for OpenALEX polite pool | Optional |
 | `DATA_DIR` | Data directory for knowledge DB | Platform-specific |
 
+!!! note "Sync Schedules"
+    Sync schedules are configured per-community in each community's `config.yaml` under the `sync` key, not via environment variables. See [Knowledge Sync](knowledge-sync.md) for details.
+
 ## Examples
 
 ### Quick Start