fix: persist pre_fix_sha, add agent output limit, fix crash bugs

[chanakyav]

Summary

Addresses three issues in one PR: crash-resilient SHA persistence (#23), agent output OOM prevention (#22), and five high-severity crash bugs at system boundaries (#73).

Changes

Issue #23 — Persist pre_fix_sha for crash recovery

• persistence.py: Schema v6 to v7. Added pre_fix_sha TEXT column, migration entry, _TASK_COLUMNS entry.
• orchestrator.py: _do_fix() and _do_fix_ci() now persist pre_fix_sha via update_task(). _do_verify_push() reads from self.task.get("pre_fix_sha") with fallback to instance variable.

Before: If orchestrator crashed between FIX and VERIFY_PUSH, pre_fix_sha was lost. On resume, new_sha != None was always True — incorrectly passing verification.

Issue #22 — Agent output size limit (max_output_bytes)

• config.py: New max_output_bytes config option (default: 50 MB, minimum: 1 MB).
• agent.py: _stream_and_capture() stops writing to StringIO when limit is exceeded, but keeps streaming to terminal. Appends [OUTPUT TRUNCATED] marker.
• orchestrator.py: Passes max_output_bytes from config to run_agent().

Before: A runaway agent printing large output could fill RAM with no cap on the StringIO buffer.

Issue #73 — High-severity crash bug fixes

1. config.py: json.load() on malformed config now raises ValueError with file path and parse details instead of raw JSONDecodeError.
2. github_api.py: get_issue() wraps json.loads() — raises GitHubAPIError on parse failure.
3. github_api.py: get_pr_description() — same pattern.
4. cli.py: cmd_start --issue catches GitHubAPIError, prints error, exits 1.
5. cli.py: Prompt file open() catches PermissionError/OSError, prints error, exits 1.

Tests Added (12 new)

• test_pre_fix_sha_persists + migration test updated (test_persistence.py)
• test_output_truncated_when_limit_exceeded (test_agent.py)
• test_output_not_truncated_when_under_limit (test_agent.py)
• test_output_unlimited_when_zero (test_agent.py)
• test_validation_max_output_bytes (test_config.py)
• test_max_output_bytes_default (test_config.py)
• test_malformed_json_config_file (test_config.py)
• test_issue_fetch_failure_exits (test_cli.py)
• test_file_permission_error_exits (test_cli.py)
• test_invalid_json_raises_api_error for get_issue (test_github_api.py)
• test_invalid_json_raises_api_error for get_pr_description (test_github_api.py)

Verification

• ruff check src/ tests/ — zero errors
• pytest tests/ — 283 tests passed, zero failures, no regressions

Closes #22, Closes #23, Closes #73

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