Add list_dir: BFS filesystem listing with gitignore and 10k-char cap

[justrach]

Graff's codedb list_dir is an in-process grok-build-style listing (BFS, .gitignore, 10k-char cap, collapsed subtree summaries) because codedb's existing ls/tree are index queries.

Port the same command into codedb itself so:

• codedb list_dir [path] works from the CLI (no index required)
• MCP codedb_list_dir lists the live filesystem, including unindexed trees
• ls/tree stay index-based

Keep output aligned with graff (github.com/justrach/codegraff) so harness and codedb evolve together.