Fix generate-config --from-setup to include sparse checkout paths

[Copilot]

generate-config --from-setup reads .gitmodules to reconstruct a submod.toml, but sparse checkout patterns live in each submodule's .git/info/sparse-checkout file — not .gitmodules — so they were silently dropped from the generated config.

Changes

• src/git_manager.rs: After reading entries from .gitmodules, iterate over each submodule path and call git_ops.get_sparse_patterns(path) to read the sparse-checkout file. Non-empty patterns are written back onto the entry before building the config.

• src/config.rs: Added SubmoduleEntries::set_sparse_paths_for(&mut self, name, paths) — updates sparse_paths on the entry in-place and keeps the parallel sparse_checkouts map in sync, avoiding a full clone-modify-update cycle.

• tests/command_contract_tests.rs: Added test_generate_config_from_setup_includes_sparse_paths — adds a submodule with --sparse-paths src,docs, runs generate-config --from-setup, and asserts the generated TOML reflects those paths.

# Before: sparse_paths silently absent
[sparse-lib]
path = "lib/sparse"
url = "file:///tmp/repo"

# After: sparse_paths correctly captured
[sparse-lib]
path = "lib/sparse"
url = "file:///tmp/repo"
sparse_paths = ["src", "docs"]

[Copilot]

Pull request overview

Fixes generate-config --from-setup so the generated submod.toml includes each submodule’s sparse checkout paths by reading them from the submodule repo’s sparse-checkout file (since this data is not stored in .gitmodules).

Changes:

• Populate sparse_paths during generate-config --from-setup by calling git_ops.get_sparse_patterns() per submodule.
• Add SubmoduleEntries::set_sparse_paths_for() to update sparse_paths and keep sparse_checkouts synchronized.
• Add a contract test asserting generated config output includes sparse_paths.

Reviewed changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated 1 comment.

File	Description
src/git_manager.rs	Augments --from-setup config generation by pulling sparse patterns from submodule sparse-checkout configuration.
src/config.rs	Adds an in-place helper to set sparse_paths while attempting to keep the parallel sparse map in sync.
tests/command_contract_tests.rs	Adds a regression test to ensure sparse paths appear in the generated TOML.

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[codecov]

Codecov Report

❌ Patch coverage is 77.77778% with 6 lines in your changes missing coverage. Please review.

Files with missing lines	Patch %	Lines
src/config.rs	64.28%	5 Missing ⚠️
src/git_manager.rs	92.30%	1 Missing ⚠️

Files with missing lines	Coverage Δ
src/git_manager.rs	88.47% <92.30%> (+0.03%)	⬆️
src/config.rs	80.81% <64.28%> (-0.17%)	⬇️

... and 2 files with indirect coverage changes

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