Add temp-clone support to run fyai on remote Git repos

[Codex]

Enable running fyai against a GitHub/GitLab repository by cloning into a temporary workspace, processing there, and leaving no residue beyond the output.

• CLI/Entry: New --repo (with optional --repo-branch) flags hook main flow to a remote-run path after normal config merge.
• Execution: repository.rs clones with git --depth 1, swaps Config.directory to the temp clone, invokes existing processing, and relies on TempDir drop for cleanup.
• Docs: README documents remote usage and new flags.
• Tests: Added coverage for remote run behavior and temp cleanup via local git fixture.

Example:

fyai --repo https://github.com/owner/repo.git --repo-branch main -o output.txt

Original prompt

add a new command that allow to perform fyai but on a github/gitlab repo instead of current local directory. code should be modular and operation shouldn't leave trace on computer except the produced result. if needed, can use a tmp dir but should cleanup. if better alternatives exist, do it.

[Copilot]

Pull request overview

Adds support for running fyai against a remote Git repository by cloning it into a temporary workspace, running the existing processing pipeline on that clone, and relying on tempdir cleanup afterward.

Changes:

• Introduces --repo and optional --repo-branch CLI flags and routes execution through a repository-clone path.
• Adds src/repository.rs with git clone --depth 1 + tempdir-based cleanup, and overrides Config.directory to point at the clone.
• Documents the new remote-run workflow in README and adds unit tests around clone/run behavior.

Reviewed changes

Copilot reviewed 7 out of 7 changed files in this pull request and generated 8 comments.

Show a summary per file

File	Description
src/repository.rs	Implements tempdir clone + runs existing pipeline on the cloned directory.
src/main.rs	Hooks --repo flow into main execution after config merge.
src/cli.rs	Adds --repo / --repo-branch flags to clap CLI.
README.md	Documents new flags and remote usage example.
src/tests/repository_tests.rs	Adds tests for running on a cloned repo and temp cleanup behavior.
src/tests/mod.rs	Registers the new repository test module.
Cargo.toml	Moves tempfile into runtime dependencies.

Comments suppressed due to low confidence (1)

Cargo.toml:28

• [dev-dependencies] is now empty after moving tempfile to normal dependencies. Consider removing the empty section to keep Cargo.toml tidy.

[dev-dependencies]

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