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docs: document preflight-dev init command and fix Node 20+ badge#122

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docs: document preflight-dev init command and fix Node 20+ badge#122
TerminalGravity wants to merge 5 commits intomainfrom
docs/add-init-command-and-fix-badge

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Covers LanceDB native binary failures, CLAUDE_PROJECT_DIR config,
vector search not returning results, MCP handshake debugging,
and performance tips. Links from README nav bar.
- examples/.preflight/config.yml: profile, related projects, thresholds, embeddings
- examples/.preflight/triage.yml: strictness, always_check/skip/cross-service keywords
- examples/.preflight/README.md: setup instructions and env var fallback reference
- README.md: link to examples from Configuration Reference section
Add shell() helper to git.ts for commands needing shell features
(pipes, redirects, ||, &&). Convert all remaining run() calls with
shell syntax across 12 tool files to use either shell() or proper
array args.

Fixes #110
@TerminalGravity
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Heads up — this bundles TROUBLESHOOTING.md and example configs that overlap with #114 and #118. Once those merge, this PR will likely have conflicts in those files. Might want to rebase and drop the overlapping files so this is purely the init command docs + badge fix.

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