Document the `~/.hub/` runtime directory tree (bare repos, transcripts) in architecture or store docs

[ooloth]

Why

A developer debugging a failed investigation or reasoning about disk usage has no way to know these directories exist, what they contain, how large they can grow, or how to reset them.

Current state

The ~/.hub/ directory and its subdirectories (~/.hub/repos/ for bare repos, ~/.hub/transcripts/ for agent transcripts) are created at runtime. store/README.md documents the SQLite database path but does not mention ~/.hub/. No architecture doc, CONTRIBUTING.md entry, or crate README references this directory tree.

Ideal state

• A docs/architecture/ file or store/README.md documents ~/.hub/ alongside the SQLite database path.
• The documentation states: what each subdirectory contains, when each is created, how large it can grow, and how to reset or prune it.

Out of scope

Implementing automated pruning (transcript retention is tracked in #82).

Starting points

• store/README.md — existing store docs to extend or link from
• docs/architecture/ — candidate location for a new runtime-dirs.md entry
• ui/tui/src/investigations/mod.rs — shows where ~/.hub/repos/ is created
• workflows/src/implement.rs — shows where ~/.hub/transcripts/ is written

QA plan

1. Open store/README.md or the relevant architecture doc — expect a section describing ~/.hub/ with its subdirectory tree, creation trigger, and reset instructions.
2. Follow the reset instructions — expect the directory to be cleared without breaking subsequent hub fetch.

Done when

A developer can learn what ~/.hub/ contains, why it exists, and how to reset it by reading one linked document from the project root.