Merge parallel SQLite rollback from origin/main

Both lines of work restored the SQLite implementation from 3c850e4. This
branch is the superset (docs-aligned CLI, REST API, pure-Go SQLite driver,
tool aliases, packaging fixes), so the merge keeps this tree; the remote
branch's new executable MCP user-flow tests and CI workflow are adopted in
the follow-up commit.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

Author: rainmana