docs: remove stale libSQL/async references

[z23cc]

Delete 3 stale reference docs, fix remaining flowctl-db refs in CLAUDE.md and docs.

🤖 Generated with Claude Code

[Copilot]

Pull request overview

Removes outdated documentation referencing the old libSQL/async-backed storage and updates remaining docs to reflect the current JSON file-based storage implementation.

Changes:

• Update storage/module references in existing docs (json_store/flowctl-core).
• Delete three stale reference docs under docs/references/.
• Update CLAUDE.md to reflect the current flowctl workspace shape and storage runtime.

Reviewed changes

Copilot reviewed 6 out of 6 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
docs/token-optimization-audit.md	Updates references from the removed DB/spec-writer implementation to flowctl-core modules.
docs/references/testing-patterns.md	Deletes a testing reference document (now risks broken internal links).
docs/references/security-checklist.md	Deletes a security checklist reference document (now risks broken internal links).
docs/references/performance-checklist.md	Deletes a performance checklist reference document (now risks broken internal links).
docs/adr-guide.md	Updates ADR example filename away from libSQL naming; still contains a broken template path.
CLAUDE.md	Updates workspace/crate count and storage runtime description to match JSON/JSONL file storage.

Comments suppressed due to low confidence (5)

docs/adr-guide.md:27

• The guide points to references/adr-template.md, but there is no docs/references/ directory (and no adr-template.md anywhere in the repo). This is a broken path for readers—either add the referenced template file (and directory), or update this line to the correct existing template location.

  ADR-001-json-file-based-storage.md
  ADR-002-wave-checkpoint-execution-model.md
  ADR-003-teams-file-locking-protocol.md

Use the template at references/adr-template.md as your starting point.

**docs/token-optimization-audit.md:207**
* This table still references a `spec_writer` component for several YAML/spec-related optimizations, but there is no `spec_writer` in the current codebase (no `spec_writer` symbol/file under `flowctl/`). Consider replacing `spec_writer` with the current owning module(s), e.g. `flowctl-core/frontmatter.rs` and/or `flowctl-core/json_store.rs`, so the audit items remain actionable.

| 21 | Remove file_path YAML field (derivable from file's own path) | flowctl-core/json_store.rs | P0 |
| 22 | Remove schema_version: 1 from every spec (only needed during migration) | spec_writer | P0 |
| 23 | Timestamps: drop microsecond precision (…313450Z → …Z) | spec_writer | P0 |
| 24 | H1 heading should not repeat full ID (# Title not # fn-15-….3 Title) | spec_writer | P0 |
| 25 | Description section should not duplicate Size/Layer/Files from YAML | spec_writer | P0 |

**docs/references/testing-patterns.md:1**
* Deleting this reference doc will break existing in-repo links: `skills/flow-code-cicd/SKILL.md` still points to `references/testing-patterns.md` (e.g., lines 24, 215, 245). Either keep/move this doc and update those links, or update the skill to point at a replacement document.
**docs/references/security-checklist.md:1**
* Deleting this checklist will break existing in-repo links: `skills/flow-code-cicd/SKILL.md` still references `references/security-checklist.md` (e.g., lines 148 and 238). Please update those references (or retain/move this checklist).
**docs/references/performance-checklist.md:1**
* Deleting this checklist will break an existing in-repo link: `skills/flow-code-performance/SKILL.md` still references `references/performance-checklist.md` (line 238). Please update that reference (or retain/move this checklist).
</details>



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[Copilot]

json_store.rs doesn't appear to define the YAML spec frontmatter schema (there are no frontmatter/Frontmatter references there); that logic lives in flowctl/crates/flowctl-core/src/frontmatter.rs. Update this reference so readers land on the actual frontmatter schema implementation.

Suggested change

	- Spec frontmatter schema: `flowctl/crates/flowctl-core/src/json_store.rs`
	- Spec frontmatter schema: `flowctl/crates/flowctl-core/src/frontmatter.rs`

[Copilot]

This doc update removes the storage DB/async references, but the PR also deletes docs/references/* docs that are still referenced by skills (e.g., skills/flow-code-cicd/SKILL.md and skills/flow-code-performance/SKILL.md). Please update those skill links (or provide replacement docs) to avoid broken internal references.