#300 fix(setup): enable reranking when API setup configures a reranker; rewrite docs

Three commits, meant to be rebase-merged.

fix(setup): retrieval.reranking_enabled defaults to false, and vera setup --api / vera backend --api never set it, so a saved API reranker (including the Qwen preset) never ran.

• API setup enables reranking exactly when a reranker is configured.
• Switching to a local backend drops the saved API reranker and turns the flag off with it (unless the shell supplies RERANKER_MODEL_*), so it does not start the slower local CPU reranker. A local reranking opt-in without a saved API reranker is kept.
• vera doctor warns (not fails) when a reranker endpoint is saved but reranking is off, covering setups made with earlier versions.
• Local model load hints link to the manual install guide instead of the stale ~/.vera/models/ path.

docs: rewrite of README, docs/, package READMEs, CONTRIBUTING, AGENT-USAGE. Corrects stale commands and paths (Docker -w /workspace, model cache layout, nonexistent commands and types) and adds v2.1.4 release notes.

Checks: cargo fmt --check, cargo clippy --workspace --all-targets -D warnings, cargo test --workspace pass locally; end-to-end vera setup --api --yes with reranker env now saves reranking_enabled = true, and vera doctor shows the new warning when it is off.

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Summary by cubic

Fixes API setup so a reranker saved by vera setup --api or vera backend --api actually runs during search, rewrites the user-facing documentation, and bumps rustls to clear the latest cargo-deny advisories.

Behavior

• API setup now turns reranking on exactly when a reranker is configured; before, the reranker was saved but never used.
• Switching back to a local backend drops the saved API reranker and turns reranking off, unless the shell supplies RERANKER_MODEL_*, so it does not start the slower local CPU reranker.
• vera doctor now warns (not fails) when a reranker is saved but reranking is off, covering setups made with earlier versions.
• Local model load errors link to the manual install guide instead of the stale ~/.vera/models/ path.

Docs

• Rewrote the README, docs/, package READMEs, CONTRIBUTING, and AGENT-USAGE to correct stale commands and paths, and added v2.1.4 release notes.
• Updated rustls to 0.23.46 for RUSTSEC-2026-0346 through 0349.

Summary by CodeRabbit

• Bug Fixes

  • API setup now enables reranking when an API reranker is configured. Clearing saved API reranker settings better preserves local reranking preferences, and vera doctor warns when a saved reranker is not active.
  • Updated local model installation errors to point to manual setup guidance.

• Documentation

  • Refreshed the main guides, command references, installation instructions, and package READMEs with clearer setup and search workflows.
  • Expanded guidance on search, supported file types, model backends, privacy, Docker, and troubleshooting.
  • Updated benchmark and migration information, including compatibility notes for existing indexes.

fix(deps): rustls 0.23.45 -> 0.23.46 for RUSTSEC-2026-0346, 0347, 0348, 0349 (cargo-deny advisories failed CI).

Docs also address the verified review-bot findings (pipeline order, scope filtering, Semble matching granularity, musl on x86_64 only, CUDA 13.1 driver, manual ONNX Runtime via ORT_DYLIB_PATH, and others).