docs: sync website + README + CLAUDE.md with current code

[jamesbrink]

Summary

A targeted audit pass to bring the docs back in sync with the code after recent changes (codex command, schema bump, src/stats.rs).

• Bumps documented schema_version from 2 → 3 to match src/index.rs:17.
• Adds src/stats.rs (the percentile_sorted helper) to the modules tables in both CLAUDE.md and website/guide/architecture.md.
• Removes completions from the src/commands/*.rs listing — it's actually a helper in main.rs, not a module file under commands/.
• Adds the missing hyperlink for codex in the README subcommands table.
• Tightens website/guide/index.md's "Every read command" bullets so they correctly call out that models, turns, prs, and files are index-only (no --no-index), and that claudex codex is a separate reader that scans ~/.codex/ and never touches the Claude Code index.
• Adds an invariant note in CLAUDE.md flagging codex as the one subcommand that bypasses the index pipeline, and lists the actual state file (state_5.sqlite) it opens.

The flag matrix in website/commands/index.md, the pricing table in website/reference/pricing.md, the schema page in website/reference/schema.md, and every per-command page were spot-checked against src/main.rs / src/types.rs / src/index.rs and found accurate; no changes needed there.

Test plan

• bun fmt:check passes
• bun run build (vitepress) builds clean
• ci-local passes (fmt-check → check → clippy → test → build), 203 tests green
• Confirm PR preview / Pages deploy renders the architecture and guide tables correctly after merge

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 79.51%. Comparing base (a4a4d0c) to head (26b44d9).

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #21      +/-   ##
==========================================
- Coverage   79.54%   79.51%   -0.04%     
==========================================
  Files          23       23              
  Lines        6166     6166              
==========================================
- Hits         4905     4903       -2     
- Misses       1261     1263       +2     

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[Copilot]

Pull request overview

This PR synchronizes documentation with the current claudex codebase, especially around schema versioning, the new stats helper module, and the Codex command’s separate data path.

Changes:

• Updates documented index schema version from 2 to 3.
• Adds src/stats.rs to architecture/module documentation.
• Clarifies command listings and flag behavior for codex, --no-index, and completions.

Reviewed changes

Copilot reviewed 4 out of 4 changed files in this pull request and generated no comments.

File	Description
website/guide/index.md	Clarifies common read-command flags and index-related caveats.
website/guide/architecture.md	Updates module table with src/stats.rs and corrected command module list.
README.md	Adds missing Codex command documentation link.
CLAUDE.md	Updates schema version, module list, and Codex index-pipeline invariant.

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