feat(doctor): report repository readiness hygiene

[SioYooo]

Summary

• Add a source-free repository readiness object to status/doctor JSON so users and agents can distinguish missing init, state-only/no-active-index, ready active index, autosync recommendation, and unhealthy/stale states.
• Report local analysis state hygiene for .repogrammar/ and foreign unmanaged .codegraph/ state without source text, absolute paths, raw Git output, or mutation.
• Update CLI, MCP guidance, specs, README, changelog, testing policy, and durable project memory.

Scope

• Documentation-only
• CLI/MCP behavior
• Analyzer/indexing behavior
• Installer/release/npm
• Telemetry/metrics
• Other: repository readiness and local-state hygiene reporting

Evidence And Boundaries

• Positive fixtures or examples: not-initialized status/doctor readiness; state-only no-active-index readiness; ready active index after default init; autosync enabled but daemon not running recommending repogrammar autosync start; storage-unhealthy readiness; .repogrammar/ ignored/tracked-risk hygiene; .codegraph/ foreign provider state.
• Negative fixtures or UNKNOWN cases preserved: readiness output remains source-free and absolute-path-free; MCP only recommends commands and stays read-only; .codegraph/ is reported as foreign unmanaged state only.
• Claims this PR does not make: no React/RN support, no expanded language support, no provider-backed semantic claims, no measured token savings, no install/init/autosync mutation from MCP, and no RepoGrammar ownership of .codegraph/.

Validation

PASS cargo fmt --all -- --check
PASS cargo clippy --workspace --all-targets --all-features -- -D warnings
PASS cargo test --workspace --all-features
PASS python3 src/workers/python/worker.test.py
PASS node src/workers/typescript/worker.test.js
PASS npm run test:npm-wrapper
PASS npm_config_cache=/private/tmp/repogrammar-npm-cache npm pack --dry-run
PASS bash src/install/repogrammar-install.test.sh
PASS cargo run --quiet --bin repo-guard -- check
PASS cargo run --quiet --bin repo-guard -- check-diff --base origin/main --head HEAD
PASS git diff --check
PASS cmp -s AGENTS.md CLAUDE.md

Release Notes

• Changelog/docs updated when public behavior changed.
• No generated junk, logs, .repogrammar/, credentials, private source, or unrelated formatting included.
• No unsupported token-saving, release/npm availability, language-support, or production-stability claims.