docs: May 25 cleanup sweep — refresh README + reference docs; remove docs/superpowers/

[jramos]

Summary

A documentation audit surfaced four classes of staleness after this week's five-PR feature ship. This PR closes the gap.

Three substantive commits:

1. docs(readme): refresh for May 23-25 feature ship; consolidate deployment section — README updates:

   • Rewrote the "Why this isn't DSPy+GEPA" section (knee-point selection is no longer a default-active callout after the val-best path stopped routing through the selector)
   • Cost estimate ~$2-10 → ~$1-5 (matches recent run data)
   • Added a Tune GEPA's search behavior subsection covering --gepa-acceptance, --gepa-minibatch-size, --knee-point-strategy
   • Consolidated the previously-overlapping "Ship the evolved skill back to source" + "Automated PR opening (opt-in)" sections into a single Shipping the evolved artifact heading with two clearly-labeled subsections for --apply/--patch (local) vs --create-pr (remote PR)

2. docs(refs): refresh dependencies, model_resolution, review_notes, interfaces for current state — reference-doc updates:

   • dependencies.md: documents the gepa git-pin + [tool.uv] override-dependencies block
   • model_resolution.md: re-verified; only timestamp bump
   • review_notes.md: retired (snapshot drifted, evergreen content already lives in AGENTS.md + components.md)
   • interfaces.md: added 7+ flag entries for the May 23-25 additions (mirrored across skill + tool sections); rewrote stale --knee-point-strategy description and --closed-loop-during-evolution "raises UsageError" claim
   • AGENTS.md: clarified the two knee-point-as-default-active claims

3. chore: remove docs/superpowers/ from repo (plans + specs are local-only); refresh schema_version + test counts; mark superseded research — convention + drift:

   • Removed docs/superpowers/ (4 plan files + 2 spec files). Design specs and implementation plans are local-only artifacts and should never have been committed.
   • Added docs/superpowers/ to .gitignore so the convention is enforced going forward
   • Fixed one dangling code-comment reference in evolution/core/saturation_check.py (pointed at a deleted spec file → now points at reports/calibration_findings.md)
   • Prepended a "Superseded" note to docs/research/knee_point_analysis.md
   • Bumped gate_decision.json schema version from "4" → "5" in 4 docs, with a new Schema v5 additions subsection enumerating the 11 new fields
   • Refreshed test count 1076 → 1166 and test-file count 55 → 61 across docs/codebase_info.md and docs/index.md

Test plan

• Full suite still passes locally: 1166 (unchanged from main, no code path changes)
• No accidental code edits: git diff main..HEAD -- 'evolution/**/*.py' returns ONLY the one-line comment fix in saturation_check.py
• Zero residual docs/superpowers/ references: grep -rn 'docs/superpowers' . --exclude-dir=.venv --exclude-dir=output returns nothing
• Zero residual stale claims for the items in scope: schema_version "4", test count 1076, knee-point-as-default-active wording all grep-clean
• CI green across 4 Python versions