[T-107] Link file references in docs

Internal ID: `T-107`

**Description**
Convert mentions of repo files in docs/*.md into GitHub-friendly hyperlinks.

**Meta**
- Status: `TODO`
- Priority: `med`
- Owner: `DOCS`
- Tags: `docs`

_This issue is synced from `.codex-swarm/tasks.json`. Change status and details in that file, not here._