refactor: remove dead code and stale references (#2575)

- Remove stale top-level `discovery.sh` reference from CLAUDE.md file
  structure (the file was never in the repo; actual script lives at
  `.claude/skills/setup-agent-team/discovery.sh`)
- Fix `autonomous-loops.md` rule that referenced `./discovery.sh --loop`
  with the correct path to the actual discovery script

No functional code changes. All 1400 tests pass, biome lint clean.

Co-authored-by: spawn-qa-bot <qa@openrouter.ai>
Co-authored-by: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-authored-by: L <6723574+louisgv@users.noreply.github.com>

.claude/rules/autonomous-loops.md

@@ -1,6 +1,6 @@
 # Autonomous Loops
 
-When running autonomous discovery/refactoring loops (`./discovery.sh --loop`):
+When running autonomous discovery/refactoring loops (`.claude/skills/setup-agent-team/discovery.sh --loop`):
 
 - **Run `bash -n` on every changed .sh file** before committing — syntax errors break everything
 - **NEVER revert a prior fix** — don't undo previously applied compatibility fixes

CLAUDE.md

@@ -46,7 +46,6 @@ spawn/
     discovery.yml                # Scheduled + issue-triggered discovery workflow
     refactor.yml                 # Scheduled + issue-triggered refactor workflow
   manifest.json                  # The matrix (source of truth)
-  discovery.sh                   # Run this to trigger one discovery cycle
   fixtures/                      # API response fixtures for testing
   README.md                      # User-facing docs
   CLAUDE.md                      # This file — project overview