[codex] Build active index by default in init

[SioYooo]

Summary

• Make repogrammar init build or refresh the active index by default, while --state-only preserves lifecycle-only repair.
• Keep --resync as an explicit spelling of the default index build and start --autosync only after the first active index succeeds.
• Update MCP guidance, quickstarts, specs, testing docs, repo memories/skills, and branch-cleanup guidance for merged/superseded branches.

Scope

• Documentation-only
• CLI/MCP behavior
• Analyzer/indexing behavior
• Installer/release/npm
• Telemetry/metrics
• Other: agent workflow and repo memory guidance

Evidence And Boundaries

• Positive fixtures or examples: init_ coverage now verifies default indexing, --yes indexing without broadening .gitignore writes, autosync-after-index sequencing, product-runtime default init indexing, and query behavior after default init.
• Negative fixtures or UNKNOWN cases preserved: --state-only --resync and --state-only --autosync fail before state creation; existing ProductCliRuntime fixture tests keep explicit index/resync generation baselines via --state-only setup.
• Claims this PR does not make: no new language/framework support, no React/RN support, no weakened UNKNOWN/staleness/source-output/telemetry gates, no installer-created .repogrammar/, no .codegraph/ management.

Validation

Paste commands and results:

cargo fmt --all -- --check
# passed
cargo clippy --workspace --all-targets --all-features -- -D warnings
# passed
cargo test --workspace --all-features
# passed: 795 lib tests passed, 1 ignored; 9 repo_guard tests passed; 58 repogrammar bin tests passed; doc-tests passed
node src/workers/typescript/worker.test.js
# passed
node src/npm/repogrammar.test.js
# passed
npm_config_cache="${TMPDIR:-/tmp}/repogrammar-npm-cache" npm pack --dry-run
# passed
python3 src/workers/python/worker.test.py
# passed
bash src/install/repogrammar-install.test.sh
# passed
cargo run --quiet --bin repo-guard -- check
# repository guard passed
cargo run --quiet --bin repo-guard -- check-diff --base origin/main --head HEAD
# diff documentation gate passed
git diff --check
# passed
cmp -s AGENTS.md CLAUDE.md
# passed

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.