fix: honor run cwd in command templates

[Bortlesboat]

Summary

• Make cortex run --cwd <dir> --command <name> pass the requested run cwd into custom command templates.
• Preserve the previous process-current-directory fallback when --cwd is not provided.
• Add an integration regression test for both code paths.

Why

This addresses PlatformNetwork/bounty-challenge#53357. The command registry already scans commands from --cwd, but {{cwd}} expansion used std::env::current_dir() instead of the run cwd override.

Verification

• cargo test -p cortex-cli --test run_command_cwd
• cargo check -p cortex-cli
• cargo fmt --check --package cortex-cli
• git diff --check

Note: cargo test -p cortex-cli run_cmd::tests::test_output_format_display is currently blocked on upstream main by an unrelated private import in src/cortex-cli/src/agent_cmd/tests.rs.

[greptile-apps]

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