fix(cli): align node lookup and command guidance

[sunerpy]

Summary

• make codegraph node and codegraph_node accept the exact node IDs returned by search --json
• activate and test MCP node line filtering, including combined file/line pins
• clarify lifecycle positional paths versus query -p/--path across CLI help, canonical Skill, installer guidance, README, and CLI/MCP docs
• remove obsolete codegraph init -i recovery guidance
• run CLI bootstrap and command execution on an explicit 8 MiB stack so Windows is not constrained by the MSVC 1 MiB main-thread default; add a one-MiB launcher regression test

Verification

• make ci
• pre-push full gate (fmt, clippy, workspace tests, guardrail)
• targeted MCP node, CLI round-trip, Skill installer, watcher guidance, MCP golden, affected-command, and constrained-stack tests
• A/B reproduction: origin/main succeeds with a 1 MiB launcher stack, the help-expanded build failed before the stack fix, and the fixed build succeeds

[codecov]

Codecov Report

❌ Patch coverage is 93.81443% with 6 lines in your changes missing coverage. Please review.

Files with missing lines	Patch %	Lines
crates/codegraph-cli/src/main.rs	76.92%	3 Missing ⚠️
crates/codegraph-mcp/src/engine.rs	95.65%	3 Missing ⚠️

❌ Your patch check has failed because the patch coverage (93.81%) is below the target coverage (95.00%). You can increase the patch coverage or adjust the target coverage.

@@           Coverage Diff           @@
##             main     #265   +/-   ##
=======================================
  Coverage   95.36%   95.37%           
=======================================
  Files         144      144           
  Lines       84347    84438   +91     
=======================================
+ Hits        80441    80529   +88     
- Misses       3906     3909    +3     

Files with missing lines	Coverage Δ
crates/codegraph-cli/src/installer/shared.rs	95.80% <100.00%> (+<0.01%)	⬆️
crates/codegraph-mcp/src/instructions.rs	100.00% <ø> (ø)
crates/codegraph-mcp/src/schemas.rs	98.63% <100.00%> (+0.05%)	⬆️
crates/codegraph-watch/src/worktree.rs	92.59% <100.00%> (+0.11%)	⬆️
crates/codegraph-cli/src/main.rs	90.92% <76.92%> (-0.04%)	⬇️
crates/codegraph-mcp/src/engine.rs	97.88% <95.65%> (-0.03%)	⬇️

... and 1 file with indirect coverage changes

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