Fix agent context files workspace root

[shiny-code-bot]

Summary

• Preserve the active workspace root on created agents so context_files resolve from the session/worktree cwd instead of the harness process cwd.
• Route run_agent and auto-review agent creation through workspace-aware creation paths.
• Add a regression test for explicit workspace roots when the process cwd differs.

Validation

• cargo test -p code-core create_agent_preserves_explicit_workspace_root_for_context_files
• cargo test -p code-core context_files
• ./build-fast.sh

This addresses the auto-review finding that context_files could misresolve or reject valid files in multi-session/worktree flows.