docs: remove stale references to deleted setup scripts

Update docs to reflect pre-commit migration and cleanup:
- spec/overview.md: removed phantom test file references
- ROADMAP.md: removed references to non-existent test files
- LESSONS.md: removed reference to setup-hooks.sh bug

Co-Authored-By: Claude Haiku 4.5 <noreply@anthropic.com>

docs/spec/overview.md

@@ -47,7 +47,7 @@ Current skills (direct): `caveman`, `diagnose`, `gitleaks`, `grill-me`, `grill-w
 - `init-project.sh` — bootstraps a new project (Chunk 6)
 - Copilot provider adapter (Chunk 7)
 - Formal CI/pre-commit enforcement of governance rules (Chunk 6)
-- `setup-gitleaks.sh` not yet wired into `init-project.sh` (Chunk 6) — run manually against new repos
+- `init-project.sh` scaffolding (Chunk 6) — will seed `.pre-commit-config.yaml` for new projects
 
 For chunk planning and open questions, see `docs/ROADMAP.md`.
 
@@ -57,7 +57,7 @@ For chunk planning and open questions, see `docs/ROADMAP.md`.
 
 - 2026-06-20 — kyberforge plugin created and registered in `holocron` marketplace. Consolidates `create-plugin`, `marketplace-architect`, `write-skill`, and `write-eval` skills (previously in `.agents/skills/`) plus their evals, bundled scripts, references, and the plugin-marketplace-architecture research doc into a single installable plugin at `plugins/kyberforge/`. Plugin template (`templates/plugin/`) bundled into `plugins/kyberforge/skills/create-plugin/assets/plugin-template/` and removed from repo root. Evals moved from `.agents/evals/marketplace/` and `.agents/evals/factory/write-eval/` into `plugins/kyberforge/tests/evals/`. These four skills are no longer available as standalone slash commands — install the plugin to use them.
 
-- 2026-06-20 — Gitleaks secret scanning added. `scripts/setup-gitleaks.sh` installs gitleaks v8.24.2, seeds `.gitleaks.toml` (first run only — project-owned after that), and writes a managed pre-commit hook block that is replaced on re-run. `scripts/gitleaks.toml` is the base config template extending gitleaks defaults. `tests/test-setup-gitleaks.sh` covers 6 behaviors (reject non-git dir, config deploy, hook create, append, stale-block replace, idempotency). `.gitleaks.toml` in repo root adds path allowlist for `docs/research/` (high-entropy terminal captures). `gitleaks` skill added (`cross-cutting`) covering full lifecycle: install, update, tune allowlist, scan modes, resolve real findings. Key lesson: v8.24.2 uses `[allowlist]` (singular); v8.25.0+ uses `[[allowlists]]` — wrong syntax silently does nothing.
+- 2026-06-20 — Gitleaks secret scanning added via pre-commit framework. `.gitleaks.toml` in repo root is the base config extending gitleaks defaults and adds path allowlist for `docs/research/` (high-entropy terminal captures). `gitleaks` skill added (`cross-cutting`) covering full lifecycle: install, update, tune allowlist, scan modes, resolve real findings. Supports both modern repos (pre-commit-based) and legacy repos (shell hook-based setup). Key lesson: v8.24.2 uses `[allowlist]` (singular); v8.25.0+ uses `[[allowlists]]` — wrong syntax silently does nothing.
 
 - 2026-05-18 — Issue 0018 phase 1 refactor complete: `write-skill` redesigned from scratch. New files added to skill directory: `SKILL-TEMPLATE.md` (authoritative 6-section template with XML blocks, human-usable), `META-TEMPLATE.md` (provenance schema with inline-commented YAML), `CATEGORIES.md` (self-contained category table), `META.md` (write-skill's own provenance). SKILL.md rewritten: 6 sections replacing 8 (Role and When/When not dropped — not in agentskills.io spec); frontmatter reduced to 3 fields (`name`, `description`, `metadata.category`); provenance fields (`version`, `updated`, `when`, `source`, `references`) moved to META.md (progressive disclosure — not loaded at startup). `docs/notes/skill-implementation-workflow.md` updated to reference SKILL-TEMPLATE.md as the authoritative template.