Separate git directory support

[chris114782]

In #200 I highlighted that the library does not support submodules.

This is because in a submodule does not store its .git folder inside the checked out repository, instead .git is a file that has a reference to the actual location of the .git directory.

This is documented here

You can manually reproduce this by doing git clone --separate-git-dir=/somewhere/else your-repo-url

This PR adds support for such a set up by detecting that .git is a file instead of a directory and attempting to read the path to the real directory from it.

[chris114782]

I was aware of the failing formatting check, but that is existing bad formatting and I was loathe to change formatting outside of code I was modifying myself.

[lyrixx]

Can you rebase your PR? thanks

[tsterker]

@chris114782 This assumes that the gitdir is a relative path, which might not be true.

[chris114782]

I'll try and take a look this weekend, it's been a few months (nearly a year now!) since I looked at this and I need to get my head back into it.

[lyrixx]

Thanks for working on this! I tested the actual code against real repositories (git init/clone --separate-git-dir=..., git worktree add, git submodule add) and found a few issues that I think block merging as-is.

Blocking: the feature doesn't work for its own headline use case

Repository::initDir() (src/Gitonomy/Git/Repository.php:173):

$foundGitPath = realpath($realGitDir . DIRECTORY_SEPARATOR . $matches[1]);

This blindly concatenates the checkout directory with the path read from the .git file. But git init/clone --separate-git-dir=<path> and git worktree add — the two use cases this PR is meant to support — always write an absolute path after gitdir: (verified with hexdump). So the join produces a bogus path like /checkout//tmp/elsewhere, realpath() returns false, and the code throws InvalidArgumentException: ... the directory it points to cannot be found even though the target directory exists.

Only the submodule case works, because git submodule add happens to write a relative path. The two cases actually named in the PR description don't.

The added test never exercises the new code path

• AbstractTest::createFoobarRepository()'s $args (containing --separate-git-dir=...) are only used inside if (null === self::$localRepository) — but self::$localRepository is a shared static cache, and provideFoobar() calls the plain variant before the (false, true) variant, so by the time the separate-git-dir call runs the cache is already populated and the branch is skipped. Even on a cold cache, the $repository object actually returned to the test (self::$localRepository->cloneTo(...)) is never given those args at all.
• Independently, tempnam(sys_get_temp_dir(), 'gitlib_') (line 81) pre-creates an empty file at that path, and git refuses to clone into a --separate-git-dir path that already exists and isn't an empty directory (fatal: repository path '...' already exists and is not an empty directory). createTempDir() in the same file already has the correct tempnam() + unlink() + mkdir() pattern for this exact problem, but it wasn't reused here.

I confirmed empirically that running BlameTest (which uses provideFoobar) passes 6/6 without ever touching initDir's new is_file() branch — so the blocking bug above ships with no test coverage at all.

• createEmptyRepository($bare = true, $separateGitDir = false) (line 42) also adds a $separateGitDir parameter that's never read in the method body — dead code.

Other real bugs

• Admin::cloneTo (src/Gitonomy/Git/Admin.php:107) — array_merge($args, $bare ? ['--bare'] : []). Since $bare defaults to true, any caller adding --separate-git-dir=... via the new $args parameter without also passing $bare = false hits fatal: options '--bare' and '--separate-git-dir' cannot be used together (verified), surfaced as an opaque RuntimeException.
• CRLF handling (Repository.php:170) — /^gitdir: ?(.+)$/ doesn't exclude \r, so a CRLF-terminated .git file leaves a trailing \r in the captured path, breaking realpath() for an otherwise valid setup.
• A permission error reading .git (e.g. chmod 000) gets silently turned into "not in the expected format" instead of surfacing the real I/O issue, since file_get_contents() returning false just makes preg_match fail to match.

Minor / cleanup

• DIRECTORY_SEPARATOR (line 173) is inconsistent with the hardcoded / used everywhere else in the same method and codebase.
• $realGitDir . '/.git' is built three separate times instead of once.
• --bare is now appended three different ways across Admin::init, cloneTo, and cloneBranchTo.
• The new .git-pointer parsing (~10 lines: regex, realpath, two exceptions) is inlined into initDir() rather than factored into a small, independently testable method — which is probably why the absolute-path and CRLF bugs went unnoticed.

Suggested direction

In initDir(), resolve $matches[1] as absolute-or-relative-to-$realGitDir (and trim the captured value) instead of unconditionally joining. For the test fixture, reuse the existing tempnam()+unlink()+mkdir() pattern from createTempDir(), and make sure the separate-git-dir args actually reach the repository object returned to the test — right now the feature this PR adds isn't actually verified by CI.