refactor: reduce cognitive complexity across 13 modules

[yacosta738]

Summary

Resolves all 28 open SonarQube Cognitive Complexity issues (rule rust:S3776) by decomposing oversized functions using the Extract Method pattern.

Motivation

All 28 issues were CRITICAL severity on SonarCloud. Each function exceeded the maximum allowed cognitive complexity of 15.

Changes

File	Issues Fixed	Key Extractions
src/update_check.rs	1	should_skip_update_check, fetch_latest_version, check_and_notify
src/config.rs	1	collect_agent_gitignore_entries, collect_target_gitignore_entries
src/commands/status.rs	1	validate_children_directory, collect_child_issues
src/commands/doctor.rs	1	6 per-check diagnostic functions
src/commands/skill.rs	3	Suggest/install renderers, URL converter
src/main.rs	1	handle_init, handle_apply, handle_clean
src/linker.rs	6	Path validators, fence detection, glob matching, clean per-type, symlink handling
src/mcp.rs	1	resolve_config_content, write_or_report_config
src/init.rs	2	Scan helpers, wizard phase extractors
src/skills/detect.rs	6	Rule evaluators, metadata collectors, workspace expanders
src/skills/suggest.rs	2	Render sections, format_installed_status
src/skills/update.rs	1	Update phase extractors
src/skills/install.rs	1	Fetch/unpack archive helpers

Verification

• ✅ cargo fmt --all -- --check
• ✅ cargo clippy --all-targets --all-features -- -D warnings
• ✅ cargo test --all-features (675 tests, 0 failures)
• ✅ make verify-all (includes JS build, docs build)

Notes

• Pure structural refactoring — zero behavior changes
• Each extracted function has a descriptive name that documents its purpose
• No new dependencies added