Layer 1: clean command support boundaries

[aboimpinto]

Summary

Refs #2791.
Refs #2870.
Reference / proof PR: #2851.

This is Layer 1 of the staged command-boundary refactor. It keeps the current command folder structure intact and focuses on cleanup before the parity-harness and group-boundary layers.

What changed

• Removed command/public helper APIs that production code no longer calls.
• Moved config persistence used by both commands and UI code into config_persistence.rs.
• Moved auto model routing used by commands, UI, runtime routing, and subagents into model_routing.rs.
• Removed stale command lookup/test-only surfaces that kept dead APIs alive.
• Hardened related tests on Windows by isolating user-global home/config state and temp Git repo line-ending behavior.
• Added .gitattributes rules so Rust sources stay LF-normalized on Windows.

What this intentionally does not do

• No command folder restructuring yet.
• No registry/parse/help split yet.
• No temporary command-by-command dual loader.
• No user_commands restructuring.

Those are tracked as later layers in #2870.

Why

#2851 showed that some behavior under commands is not command-owned. Config persistence and model routing are used by UI/runtime/subagent paths too, so keeping them under commands makes ownership blurry. This layer moves that shared behavior to neutral TUI modules and removes dead command APIs before we add the parity harness and then reshape the command boundary.

Validation

• cargo test --workspace
• Full test log scan: warning_count=0
• Full test log scan: actual_failures=0
• git diff --check

Paulo Aboim Pinto

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[github-actions]

Thanks @aboimpinto for taking the time to contribute.

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[gemini-code-assist]

Code Review

This pull request refactors the codebase by extracting configuration persistence and model routing logic into dedicated modules (config_persistence and model_routing), cleaning up unused functions and dead code across commands and skills, and configuring core.autocrlf to false in git-related tests to ensure cross-platform stability. Additionally, the parent directory search for project context files is now capped at the home directory. The review feedback highlights opportunities to optimize path traversal in project_context.rs by replacing redundant, repeated filesystem canonicalization calls inside loops with direct equality checks on pre-canonicalized paths.

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