Derive store_dir from watched_dir instead of the cwd

[Neverdecel]

The index store location defaulted to <cwd>/.coderag, computed independently
of the watched dir. This was a silent footgun: coderag index --watched-dir /home/me wrote the index to /home/me/.coderag only when you happened to run
it from /home/me; running coderag status/search from any other directory
then looked at a different (usually empty) .coderag and reported nothing —
even though a fully built index existed elsewhere.

Default store_dir to <watched_dir>/.coderag (resolved in __post_init__)
so the index lives next to the code it indexes and is found regardless of the
current working directory. An explicit --store-dir / CODERAG_STORE_DIR
still wins, and overriding watched_dir alone now moves an auto-derived store
with it. Behavior is unchanged for the common case of running inside the repo
you're indexing (watched_dir defaults to cwd).

Updates the CLI help, docs, AGENTS.md, and example.env, and adds regression
tests covering cwd-independence, explicit overrides, the env var, and
watched_dir re-pointing.

Co-Authored-By: Claude Opus 4.8 (1M context) noreply@anthropic.com
Claude-Session: https://claude.ai/code/session_01JthREmD1twWpEgHJCV9r8v

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