fix: disable sparse checkout cone mode to prevent root file leaks

[abnegate]

Summary

• Git 2.37+ defaults to cone mode for sparse checkout, which always includes root-level files alongside the specified subdirectory
• This causes VCS function deployments with a non-root providerRootDirectory to include root-level files (e.g. build.gradle.kts, package.json) that can break function builds
• Affected since Appwrite 1.5.0 (ships Git 2.43.0), including Cloud (1.9.0 ships Git 2.52.0)
• Fix: set core.sparseCheckoutCone false before writing the sparse-checkout pattern

Test plan

• Existing testGenerateCloneCommand* tests pass (pattern * clones everything regardless of cone mode)
• VCS deployment with nested providerRootDirectory no longer includes root-level files

[greptile-apps]

Greptile Summary

This PR fixes a regression in Git 2.37+ where cone mode for sparse checkout became the default, causing root-level files to always be included alongside the specified providerRootDirectory. The fix inserts git config core.sparseCheckoutCone false into the command sequence before the sparse-checkout pattern is written, but only when the target is a subdirectory (not the wildcard * pattern).

Confidence Score: 5/5

Safe to merge — targeted, minimal fix with no side effects on the wildcard (*) code path.

The change is small and surgical: one new boolean derived from an already-escaped variable, one conditional config command, and a cosmetic refactor of the array build. The $isSubdirectory comparison is correct ($rootDirectory is already escaped, so comparing against escapeshellarg('*') is the right approach). Cone mode is only disabled when it would actually cause a problem (specific subdirectory path), leaving the * path unaffected. No P1 or P0 findings.

No files require special attention.

Important Files Changed

Filename	Overview
src/VCS/Adapter/Git/GitHub.php	Adds core.sparseCheckoutCone false before writing the sparse-checkout pattern when a specific subdirectory is targeted, preventing Git 2.37+ cone-mode defaults from pulling in root-level files.

_{Reviews (2): Last reviewed commit: "(fix): only disable cone mode for subdir..." | Re-trigger Greptile}