fix(db): resolve directory paths in findDbPath to .codegraph/graph.db (#1706)

* fix(db): resolve directory paths in findDbPath to .codegraph/graph.db

When --db is passed a directory (the documented usage), findDbPath returned
the directory verbatim. SQLite then threw "disk I/O error" trying to open a
directory as a database file — breaking every read command (stats, query,
map, cycles, triage, etc.) while build was unaffected (pipeline.ts appends
the path itself).

Fix: detect if the resolved path is an existing directory and append
.codegraph/graph.db, matching the layout that `build` creates. Paths that
are explicit file paths or don't exist yet are returned unchanged.

Closes #1705

* fix(db): handle .codegraph dir input and fix config-root derivation (#1706)

Two bugs in directory-path handling for --db:

1. When the caller passes the .codegraph directory itself
   (e.g. --db /repo/.codegraph), findDbPath was treating it as
   a repo root and returning /repo/.codegraph/.codegraph/graph.db.
   Now detects basename === '.codegraph' and appends only graph.db.

2. rootDir derivation in openRepo/openReadonlyWithNative was computing
   path.dirname(path.dirname(path.resolve(customDbPath))) on the raw
   input, so --db /path/to/repo stripped two levels off the repo dir
   (yielding /path) instead of the repo root. Fixed by deriving rootDir
   from the already-resolved findDbPath output.

Add two unit tests covering both edge cases.

Impact: 3 functions changed, 133 affected

Author: carlos-alm