* fix(cli): keep GitNexus ignores inside .gitnexus
Avoid mutating analyzed repositories' root .gitignore while keeping generated GitNexus state untracked via .gitnexus/.gitignore.
Made-with: Cursor
* fix(cli): also use git info exclude for GitNexus storage
When an analyzed repo has a real .git directory, add .gitnexus/ to .git/info/exclude so local Git metadata ignores generated storage without touching root .gitignore.
Made-with: Cursor
* fix(cli): keep skip-git subdir indexes ignored
Ensure full analyze always writes the internal GitNexus ignore file so parent Git repositories stay clean for --skip-git subdirectory indexes.
Made-with: Cursor
Addresses all review items from @magyargergo and Copilot:
1. **Rename --no-git to --skip-git**: Commander.js treats --no-X flags
as negation of --X (stores as options.git = false, not options.noGit).
--skip-git maps correctly to options.skipGit.
2. **Fix false " Already up to date\ on non-git folders**: When
currentCommit is empty string, skip the cache check — we cannot
detect changes without git, so always rebuild.
3. **Replace isGitRepo() with hasGitDir()**: Use filesystem check
(statSync on .git) instead of shelling out to git CLI. Consistent,
faster, and works when git is not installed.
4. **Fix misleading warning**: Message now only fires when .git
directory is actually absent (not when git CLI fails).
5. **Add CLI integration tests**: Verify Commander maps --skip-git
correctly and that non-git folders are rejected without the flag.
