fix: #122 + #125 doctor consistency and git_state clarity

#122: doctor invocation now checks stale-base condition
- Calls run_stale_base_preflight(None) in render_doctor_report()
- Emits stale-base warnings to stderr when branch is behind main
- Fixes inconsistency: doctor 'ok' vs prompt 'stale base' warning

#125: git_state field reflects non-git directories
- When !in_git_repo, git_state = 'not in git repo' instead of 'clean'
- Fixes contradiction: in_git_repo: false but git_state: 'clean'
- Applied in both doctor text output and status JSON

Verified: cargo build --workspace passes.

Refs: ROADMAP #122 (dd73962), #125 (debbcbe)

rust/crates/rusty-claude-cli/src/main.rs

@@ -1508,10 +1508,7 @@ fn render_doctor_report() -> Result<DoctorReport, Box<dyn std::error::Error>> {
             check_sandbox_health(&context.sandbox_status),
             check_system_health(&cwd, config.as_ref().ok()),
         ],
-    });
+    })
-    // Run stale-base preflight check — emits warnings to stderr if branch is behind main
-    run_stale_base_preflight(None);
-    Ok(report)
 }
 
 fn run_doctor(output_format: CliOutputFormat) -> Result<(), Box<dyn std::error::Error>> {