github-code-review worker: comprehensive fixes for signal handling, reliability, and safety

CRITICAL fixes:
- Add pcntl_async_signals(true) before signal handlers - enables Ctrl-C to fire during exec()
- Fix $running checks in checkoutBranch to be BEFORE exec() calls, not just after
- Add missing getPRDiff() and applyPRDiff() functions with proper temp file cleanup
- Consolidate getPRHeadBranch/getPRBaseBranch into getPRRef() with retry logic

MAJOR fixes:
- Assign new UUID on job requeue - prevents infinite retry loops on same job ID
- Fix file_get_contents() false checks - prevent type mismatches
- Add try/finally cleanup for temp files in getFileDiff - prevents disk leaks
- Add repo path validation with regex and realpath() - prevents path traversal

MINOR improvements:
- Add PHPStan ignore comments for !$running (signal handler mutation)
- Add initGitRepo error checking and logging
- Add $hadValidParse flag to distinguish 'no issues' vs 'parse failed'
- Create runCommandWithTimeout() helper with proc_open + stream_select
- Extract cleanupCheckout() helper to eliminate duplicated cleanup code

BUG fixes from review:
- Fix undefined $actualBaseBranch when base branch lookup returns null
- Add file_put_contents error checks in processIssue to handle disk failures

Author: detain