Enable WAL mode for SQLite knowledge databases

[neuromechanist]

Problem

All knowledge sync operations (GitHub, Discourse, papers, docstrings) write to the same SQLite database per community. SQLite's default journal mode (delete) only allows one writer at a time, causing sqlite3.OperationalError: database is locked when multiple syncs run concurrently.

This forces all sync operations to run serially per community, significantly increasing total sync time.

Proposed Solution

Enable WAL (Write-Ahead Logging) mode on knowledge databases:

conn.execute("PRAGMA journal_mode=WAL")

WAL mode allows concurrent readers and a single writer without blocking, and multiple writers will wait (with configurable timeout) rather than immediately failing.

Implementation

• Set WAL mode in get_db_connection() or equivalent in src/knowledge/db.py
• Set a reasonable busy_timeout (e.g., 30 seconds): conn.execute("PRAGMA busy_timeout=30000")
• WAL mode persists per database file (only needs to be set once)
• Add a migration or startup check to enable WAL on existing databases

Benefits

• Parallel sync operations per community (GitHub + Discourse + papers simultaneously)
• Faster total sync time
• No more database is locked errors during normal operation

Considerations

• WAL mode creates -wal and -shm sidecar files (need to be included in backups)
• Slightly more disk usage
• Works fine with SQLite 3.7+ (all modern Python versions)

Context

Discovered during MNE community onboarding where GitHub, Discourse, and papers syncs all need to write to the same database. Currently we must run them serially to avoid lock errors.