ℹ️ About Codex in GitHub

\\n
\\n\\n[Your team has set up Codex to review pull requests in this repo](https://chatgpt.com/codex/cloud/settings/general). Reviews are triggered when you\\n- Open a pull request for review\\n- Mark a draft as ready\\n- Comment \\\"@codex review\\\".\\n\\nIf Codex has suggestions, it will comment; otherwise it will react with 👍.\\n\\n\\n\\n\\nCodex can also answer questions or update the PR. Try commenting \\\"@codex address that feedback\\\".\\n \\n

\",\"path\":null,\"side\":null,\"line\":null}","text_elements",[],{"_418":750,"_399":400,"_420":406},{"_421":751,"_423":-5,"_41":-5,"_424":-5,"_95":322,"_91":426},[752],{"_45":746,"_91":753},"input_text",{"_418":755,"_399":400,"_420":406},{"_421":756,"_423":-5,"_41":-5,"_424":-5,"_95":322,"_91":426},[757],{"_45":758,"_91":753},"\n /workspace/codex-environment-backup\n bash\n 2026-05-20\n Etc/UTC\n",{"_418":760,"_399":400,"_420":406},{"_421":761,"_423":-5,"_41":-5,"_424":-5,"_95":762,"_91":426},[763,764],"developer",{"_45":766,"_91":753},{"_45":765,"_91":753},"\n## Skills\nA skill is a set of local instructions to follow that is stored in a `SKILL.md` file. Below is the list of skills that can be used. Each entry includes a name, description, and file path so you can open the source for full instructions when using a specific skill.\n### Available skills\n- imagegen: Generate or edit raster images when the task benefits from AI-created bitmap visuals such as photos, illustrations, textures, sprites, mockups, or transparent-background cutouts. Use when Codex should create a brand-new image, transform an existing image, or derive visual variants from references, and the output should be a bitmap asset rather than repo-native code or vector. Do not use when the task is better handled by editing existing SVG/vector/code-native assets, extending an established icon or logo system, or building the visual directly in HTML/CSS/canvas. (file: /opt/codex/skills/.system/imagegen/SKILL.md)\n- openai-docs: Use when the user asks how to build with OpenAI products or APIs and needs up-to-date official documentation with citations, help choosing the latest model for a use case, or model upgrade and prompt-upgrade guidance; prioritize OpenAI docs MCP tools, use bundled references only as helper context, and restrict any fallback browsing to official OpenAI domains. (file: /opt/codex/skills/.system/openai-docs/SKILL.md)\n- plugin-creator: Create and scaffold plugin directories for Codex with a required `.codex-plugin/plugin.json`, optional plugin folders/files, and baseline placeholders you can edit before publishing or testing. Use when Codex needs to create a new local plugin, add optional plugin structure, or generate or update repo-root `.agents/plugins/marketplace.json` entries for plugin ordering and availability metadata. (file: /opt/codex/skills/.system/plugin-creator/SKILL.md)\n- skill-creator: Guide for creating effective skills. This skill should be used when users want to create a new skill (or update an existing skill) that extends Codex's capabilities with specialized knowledge, workflows, or tool integrations. (file: /opt/codex/skills/.system/skill-creator/SKILL.md)\n- skill-installer: Install Codex skills into $CODEX_HOME/skills from a curated list or a GitHub repo path. Use when a user asks to list installable skills, install a curated skill, or install a skill from another repo (including private repos). (file: /opt/codex/skills/.system/skill-installer/SKILL.md)\n### How to use skills\n- Discovery: The list above is the skills available in this session (name + description + file path). Skill bodies live on disk at the listed paths.\n- Trigger rules: If the user names a skill (with `$SkillName` or plain text) OR the task clearly matches a skill's description shown above, you must use that skill for that turn. Multiple mentions mean use them all. Do not carry skills across turns unless re-mentioned.\n- Missing/blocked: If a named skill isn't in the list or the path can't be read, say so briefly and continue with the best fallback.\n- How to use a skill (progressive disclosure):\n 1) After deciding to use a skill, open its `SKILL.md`. Read only enough to follow the workflow.\n 2) When `SKILL.md` references relative paths (e.g., `scripts/foo.py`), resolve them relative to the skill directory listed above first, and only consider other paths if needed.\n 3) If `SKILL.md` points to extra folders such as `references/`, load only the specific files needed for the request; don't bulk-load everything.\n 4) If `scripts/` exist, prefer running or patching them instead of retyping large code blocks.\n 5) If `assets/` or templates exist, reuse them instead of recreating from scratch.\n- Coordination and sequencing:\n - If multiple skills apply, choose the minimal set that covers the request and state the order you'll use them.\n - Announce which skill(s) you're using and why (one short line). If you skip an obvious skill, say why.\n- Context hygiene:\n - Keep context small: summarize long sections instead of pasting them; only load extra files when needed.\n - Avoid deep reference-chasing: prefer opening only files directly linked from `SKILL.md` unless you're blocked.\n - When variants exist (frameworks, providers, domains), pick only the relevant reference file(s) and note that choice.\n- Safety and fallback: If a skill can't be applied cleanly (missing files, unclear instructions), state the issue, pick the next-best approach, and continue.\n","\nFilesystem sandboxing defines which files can be read or written. `sandbox_mode` is `danger-full-access`: No filesystem sandboxing - all commands are permitted. Network access is enabled.\nApproval policy is currently never. Do not provide the `sandbox_permissions` for any reason, commands will be rejected.\n","turn/started",{"_399":400,"_86":769},{"_102":-5,"_41":406,"_407":770,"_409":410,"_411":771},[],"inProgress",{"_411":773,"_399":400},{"_774":775,"_91":776},"activeFlags",[],"active","thread/started",{"_779":780},"thread",{"_781":-5,"_782":-5,"_783":784,"_785":410,"_450":451,"_786":15,"_787":-5,"_788":-5,"_41":400,"_789":790,"_180":-5,"_160":791,"_792":198,"_455":793,"_411":794,"_76":795,"_796":410},"agentNickname","agentRole","cliVersion","0.124.0","createdAt","ephemeral","forkedFromId","gitInfo","modelProvider","openai","/opt/codex/sessions/2026/05/20/rollout-2026-05-20T08-54-23-019e4497-daac-76f0-a8c1-aa6eb978ec5d.jsonl","preview","vscode",{"_91":415},[],"updatedAt",[],"messages",[800],{"_41":801,"_802":803,"_804":805,"_806":805,"_421":807,"_411":808,"_423":-5,"_809":31,"_810":811,"_812":813,"_814":-5},"184fdaf6-241d-45c6-9c0e-33bc7d8f15c4","author",{"_95":322,"_180":-5,"_810":823},"create_time",1779267262.458156,"update_time",{"_819":45,"_820":821},"finished_successfully","weight","metadata",{"_815":816},"recipient","all","channel","l1239dk1",{"_817":818},"inline_comments",[],"content_type","parts",[822],"@codex address that feedback. Please count files and bytes under pruned excluded directories in the size report without including file contents or changing restore safety behavior. (path=src/agent_environment_backup/core.py line=652 side=RIGHT)\nAdd size-aware reporting and safe exclusions for rebuildable runtime/cache paths\n\n### Motivation\n- Backups were including large rebuildable runtime/cache data silently, inflating expanded backup directories and making size drivers invisible to users. \n- The intent is to keep restore safety unchanged while making exclusions explicit and surfacing size information so users can choose compact vs forensic backups.\n\n### Description\n- Add a `SIZE_REPORT_LIMIT` constant and compute per-backup size metadata including `bytes` total, `top_files_by_size`, and `top_directories_by_size` during `create_backup` and write them into the manifest under `size_report` and `counts.bytes`. \n- Record excluded/skipped entries when `iter_source_files` omits files for exclusion by appending `{\n\n------\n[Codex Task](https://chatgpt.com/codex/cloud/tasks/task_e_6a0d727c0fe48333b696d871aab713ba)\nComments in the same thread:\n\n**_{_{![P2 Badge](https://img.shields.io/badge/P2-yellow?style=flat)}} Count pruned excluded directories in size report**\n\n`excluded_entries`/`excluded_bytes` are derived from `skipped`, but this block only appends entries for excluded files that are still reached in `file_names`. In the same function, excluded directories are removed from `dir_names` before traversal, so files under newly excluded paths like `cache/`, `packages/`, `standalone/`, and `node_modules/` are never visited and therefore never counted. This makes the new size report systematically understate excluded data (often reporting `0` bytes) when exclusions happen at directory level, which defeats the purpose of surfacing size drivers.\n\nUseful? React with 👍 / 👎.\n\n### 💡 Codex Review\n\nHere are some automated review suggestions for this pull request.\n\n**Reviewed commit:** `d6dd97b6f8`\n \n\n

ℹ️ About Codex in GitHub

\n
\n\n[Your team has set up Codex to review pull requests in this repo](https://chatgpt.com/codex/cloud/settings/general). Reviews are triggered when you\n- Open a pull request for review\n- Mark a draft as ready\n- Comment \"@codex review\".\n\nIf Codex has suggestions, it will comment; otherwise it will react with 👍.\n\n\n\n\nCodex can also answer questions or update the PR. Try commenting \"@codex address that feedback\".\n \n

",{},"created",1779267334.7764893,"Completing the task","event_type","info",{"_91":426,"_95":92,"_421":2309},{"_91":855,"_856":857},{"_91":832,"_833":515,"_834":835,"_836":837,"_838":-5},"pr","pr_title","pr_message","### Motivation\n- The size report undercounts excluded data when exclusions remove whole directories from traversal, so directory-level exclusions like `cache/` or `node_modules/` report zero bytes and hide size drivers.\n\n### Description\n- Add `excluded_subtree_stats` inside `iter_source_files` to walk pruned excluded directories and compute `file_count` and `bytes` for each excluded subtree without reading file contents. \n- When a directory is identified as excluded (before `dir_names` is pruned) append an `excluded` entry to `skipped` containing `relative_path`, `reason`, `file_count`, and `bytes`. \n- Compute `size_report.excluded_entries` from summed `file_count` values (defaulting to `1` for single-file exclusions) and keep `size_report.excluded_bytes` aggregated from skipped entries. \n- Update the backup summary line to report the corrected excluded entry count and add these fields into the written `manifest.json`. \n\n### Testing\n- Ran the full test suite with `python -m pytest -q`. \n- All tests passed: `70 passed`.","output_diff",{"_91":836,"_839":195,"_127":128,"_840":-5,"_321":841,"_842":843,"_844":721,"_845":846,"_847":327,"_848":849,"_850":851},"pre_apply_patch","repo_id","preapply_patch_base_commit_sha","diff --git a/src/agent_environment_backup/core.py b/src/agent_environment_backup/core.py\nindex a9ad4258350bf942054335f1dd97cfaa1e8529fe..7e4cc32d2a4b542f889446745b8c5d8268e4c07d 100644\n--- a/src/agent_environment_backup/core.py\n+++ b/src/agent_environment_backup/core.py\n@@ -605,60 +605,91 @@ def doctor_codex_environment(\n \n def error_relative_path(base: Path, raw_path: object) -> str:\n if not raw_path:\n return \".\"\n path = Path(str(raw_path))\n try:\n return normalize_relative(path.resolve(strict=False).relative_to(base.resolve(strict=False)))\n except (OSError, ValueError):\n return str(path)\n \n \n def walk_error_entry(base: Path, exc: OSError, *, method: str) -> dict[str, str]:\n return {\n \"relative_path\": error_relative_path(base, getattr(exc, \"filename\", None)),\n \"method\": method,\n \"error\": str(exc),\n }\n \n \n def iter_source_files(\n home: Path,\n errors: list[dict[str, str]] | None = None,\n extra_excluded_dirs: frozenset[str] = frozenset(),\n skipped: list[dict[str, str]] | None = None,\n ) -> Iterator[tuple[Path, Path]]:\n+ def excluded_subtree_stats(path: Path) -> tuple[int, int]:\n+ file_count = 0\n+ total_bytes = 0\n+ for walk_root, _, walk_files in os.walk(path):\n+ walk_root_path = Path(walk_root)\n+ for walk_file in walk_files:\n+ walk_path = walk_root_path / walk_file\n+ file_count += 1\n+ try:\n+ total_bytes += walk_path.stat().st_size\n+ except OSError:\n+ pass\n+ return file_count, total_bytes\n+\n def onerror(exc: OSError) -> None:\n entry = walk_error_entry(home, exc, method=\"walk\")\n if errors is not None:\n errors.append(entry)\n return\n raise BackupError(entry[\"error\"])\n \n for root, dir_names, file_names in os.walk(home, onerror=onerror):\n root_path = Path(root)\n rel_root = root_path.relative_to(home)\n+ excluded_dirs = [\n+ name\n+ for name in dir_names\n+ if is_excluded(rel_root / name, extra_excluded_dirs)\n+ ]\n+ if skipped is not None:\n+ for excluded_dir in excluded_dirs:\n+ excluded_path = root_path / excluded_dir\n+ file_count, total_bytes = excluded_subtree_stats(excluded_path)\n+ skipped.append(\n+ {\n+ \"relative_path\": normalize_relative(rel_root / excluded_dir),\n+ \"reason\": \"excluded\",\n+ \"file_count\": file_count,\n+ \"bytes\": total_bytes,\n+ }\n+ )\n dir_names[:] = [\n name for name in dir_names\n if not is_excluded(rel_root / name, extra_excluded_dirs)\n ]\n for file_name in file_names:\n source = root_path / file_name\n relative = source.relative_to(home)\n if is_excluded(relative, extra_excluded_dirs):\n if skipped is not None:\n entry = {\n \"relative_path\": normalize_relative(relative),\n \"reason\": \"excluded\",\n }\n try:\n entry[\"bytes\"] = source.stat().st_size\n except OSError:\n pass\n skipped.append(entry)\n continue\n try:\n skip_reason = regular_file_skip_reason(source)\n except OSError as exc:\n entry = walk_error_entry(home, exc, method=\"stat\")\n entry[\"relative_path\"] = normalize_relative(relative)\n if errors is not None:\n@@ -1434,99 +1465,100 @@ def create_backup(\n )\n \n total_backup_bytes = sum(entry[\"bytes\"] for entry in entries)\n top_files_by_size = sorted(\n (\n {\n \"relative_path\": entry[\"relative_path\"],\n \"bytes\": entry[\"bytes\"],\n }\n for entry in entries\n ),\n key=lambda item: item[\"bytes\"],\n reverse=True,\n )[:SIZE_REPORT_LIMIT]\n directory_sizes: dict[str, int] = {}\n for entry in entries:\n rel_path = Path(entry[\"relative_path\"])\n for parent in rel_path.parents:\n key = \".\" if str(parent) == \".\" else normalize_relative(parent)\n directory_sizes[key] = directory_sizes.get(key, 0) + entry[\"bytes\"]\n top_directories_by_size = [\n {\"relative_path\": path, \"bytes\": size}\n for path, size in sorted(directory_sizes.items(), key=lambda item: item[1], reverse=True)[:SIZE_REPORT_LIMIT]\n ]\n excluded_skipped = [item for item in skipped if item.get(\"reason\") == \"excluded\"]\n+ excluded_entries = sum(int(item.get(\"file_count\", 1)) for item in excluded_skipped)\n excluded_bytes = sum(int(item.get(\"bytes\", 0)) for item in excluded_skipped)\n \n sensitive_note = _make_sensitive_note(profile.display_name)\n doctor_report = doctor_environment(home, profile=profile, run_commands=run_doctor_commands)\n manifest = {\n \"schema_version\": 1,\n \"created_at\": utc_now_iso(),\n \"profile\": profile.name,\n \"home\": str(home),\n \"backup_name\": backup_name,\n \"archive_format\": archive_format if make_archive else None,\n \"sensitive_note\": sensitive_note,\n \"platform\": doctor_report[\"platform\"],\n \"exclusions\": {\n \"directory_names\": sorted(EXCLUDED_DIR_NAMES | set(profile.extra_excluded_dirs)),\n \"live_sqlite_suffixes\": list(LIVE_SQLITE_SUFFIXES),\n },\n \"entries\": entries,\n \"errors\": errors,\n \"skipped\": skipped,\n \"counts\": {\n \"files\": len(entries),\n \"bytes\": total_backup_bytes,\n \"sqlite_databases\": sum(1 for entry in entries if entry[\"method\"] == \"sqlite_backup\"),\n \"errors\": len(errors),\n \"skipped\": len(skipped),\n },\n \"size_report\": {\n \"top_files_by_size\": top_files_by_size,\n \"top_directories_by_size\": top_directories_by_size,\n- \"excluded_entries\": len(excluded_skipped),\n+ \"excluded_entries\": excluded_entries,\n \"excluded_bytes\": excluded_bytes,\n },\n }\n write_json(backup_dir / \"manifest.json\", manifest)\n write_json(backup_dir / \"sqlite-integrity-check.json\", sqlite_checks)\n write_json(backup_dir / \"doctor-report.json\", doctor_report)\n write_environment_snapshot(backup_dir / \"environment-snapshot.txt\", doctor_report, profile.display_name)\n \n ok = not errors and all(check.get(\"ok\") for check in sqlite_checks)\n summary_lines = [\n f\"{profile.display_name} environment backup\",\n f\"Backup: {backup_dir}\",\n f\"{profile.display_name} home: {home}\",\n f\"Files: {len(entries)}\",\n f\"Expanded size (files only): {total_backup_bytes} bytes\",\n f\"SQLite databases: {manifest['counts']['sqlite_databases']}\",\n f\"Errors: {len(errors)}\",\n- f\"Excluded entries: {len(excluded_skipped)} ({excluded_bytes} bytes)\",\n+ f\"Excluded entries: {excluded_entries} ({excluded_bytes} bytes)\",\n f\"Integrity: {'ok' if all(check.get('ok') for check in sqlite_checks) else 'failed'}\",\n \"Restore kit: RESTORE.md, RESTORE_INSTRUCTIONS.txt, restore-environment.cmd, restore-environment.ps1, restore-environment.command, restore-environment.sh\",\n \"\",\n sensitive_note,\n ]\n (backup_dir / \"backup-summary.txt\").write_text(\n \"\\n\".join(summary_lines) + \"\\n\", encoding=\"utf-8\"\n )\n \n restore_kit = write_restore_kit(backup_dir, profile.display_name)\n \n archive_path = None\n sha256_path = None\n archive_sha256 = None\n if make_archive:\n archive_path = create_archive(backup_dir, archive_format)\n archive_sha256 = sha256_file(archive_path)\n sha256_path = archive_path.with_name(f\"{archive_path.name}.sha256\")\n sha256_path.write_text(f\"{archive_sha256} {archive_path.name}\\n\", encoding=\"utf-8\")\n \n return {\n \"ok\": ok,\n \"backup_dir\": str(backup_dir),\n \"archive\": str(archive_path) if archive_path else None,\n \"archive_sha256\": archive_sha256,\n","external_storage_diff",{"_852":853,"_854":-5},"files_modified","lines_added",34,"lines_removed","commit_message","Count pruned excluded directories in size report","additional_parent_commit_shas",[],"file_id","file_000000007a30722fb5f88cebed626082","ttl","partial_repo_snapshot","files",[858],{"_160":859,"_860":-5,"_861":862,"_863":-5},"src/agent_environment_backup/core.py","contents","line_range_contents",[864],"missing_reason",{"_865":721,"_866":867,"_421":868,"_869":57},"line_range_start","line_range_end",2061,[870,198,871,872,873,874,875,876,877,878,879,880,881,882,883,884,885,886,887,888,889,890,198,891,892,893,894,198,198,895,896,897,898,899,900,901,902,903,198,904,905,906,907,908,909,198,910,911,912,913,914,915,198,198,916,917,918,919,920,921,922,923,924,925,926,927,928,929,930,198,198,931,932,198,198,933,934,198,198,935,936,198,198,937,938,939,940,941,942,943,944,945,946,947,948,949,198,198,950,951,198,198,952,941,942,953,954,955,956,957,198,198,198,958,941,942,959,960,961,962,963,198,964,965,966,967,968,969,198,198,970,971,198,198,972,973,974,975,976,977,978,967,979,980,198,198,981,982,198,198,983,984,985,986,987,988,989,198,198,990,991,992,993,994,995,198,198,996,997,998,198,198,999,1000,1001,1002,1003,1004,1005,1006,1007,1008,1009,1010,198,198,1011,1012,1013,1014,1015,1016,1017,1018,1019,1020,1021,1022,1023,1024,1025,965,1026,1027,1028,1029,1030,1031,1032,1033,1034,1021,1022,1035,1036,1037,1038,1025,1039,1021,1022,1040,1041,1025,1042,1043,1044,1045,1046,1047,1048,1049,1050,1051,1052,1053,1054,1055,1056,1057,1058,198,198,1059,1060,1061,965,1062,1063,1064,1065,1066,198,1067,1068,1069,1070,1071,1072,1073,1074,1075,1076,1077,1078,1079,1080,1081,198,1068,1082,1083,1084,1085,1086,1087,1088,1079,1089,1090,198,1091,1092,1093,1094,1095,1096,1097,1025,198,1098,1099,1100,1101,1102,1103,1104,1105,1106,1107,1108,1109,1110,198,198,1111,1112,1113,1114,1021,1115,1116,1117,1118,1119,1025,198,1120,1121,1122,1123,1124,1125,1126,1127,1128,1129,1130,1131,1124,1125,1132,1133,1134,1127,1128,1135,1136,1137,1138,1139,1140,1046,198,198,1141,1142,1042,1143,1144,1046,1145,1146,1147,1148,1149,1150,1146,965,1151,1152,1153,1154,1146,198,1155,1156,1157,1158,1159,1160,1161,1162,1163,1164,1165,1127,1166,1167,1168,1169,1170,1171,1172,1173,1174,1175,1025,915,1058,198,198,1176,198,198,1177,1178,1042,1179,1144,1046,1145,1146,1147,965,1180,1181,1153,1154,1146,1065,1153,1182,1146,1183,1184,1185,1186,1187,1188,1189,1190,1191,1192,1193,1194,1195,1058,198,198,1196,1197,1198,1199,1200,1201,1202,1203,1204,1205,1206,1207,1208,1209,1210,1211,1212,1213,909,198,1214,1215,1216,1217,1218,1219,1220,1221,1204,1222,1223,1224,1208,1225,1226,1227,1228,1229,909,198,1230,1231,1232,902,198,198,1233,1234,974,1018,1235,1236,1237,1238,1239,198,1240,1241,198,1242,1243,1244,1245,1246,1247,1248,1249,1250,1246,1033,1251,198,198,1252,1253,1254,198,198,1255,939,1015,938,1256,1018,941,942,1257,1258,1259,1260,1261,1262,1263,1264,1265,1266,1267,1268,1269,1270,1271,1272,1273,1274,1275,1046,198,1276,1277,1278,1279,1280,1281,1282,1283,1284,1285,198,1286,1287,1288,1289,1006,1290,1291,198,1292,1293,1294,1295,1296,1297,1298,1128,1299,1300,1301,1302,1303,1304,1305,1306,1307,1108,1308,1309,1305,1306,1307,1108,1310,1311,1312,1313,1127,1314,1315,1316,1317,1318,1319,1320,1046,1321,1322,198,198,1323,1324,1015,1256,1018,1325,198,198,1326,1327,1328,1329,965,1330,1331,1332,198,198,1333,1135,1334,1335,1336,1046,198,198,1337,1338,1339,974,1340,1341,1342,1343,1344,1345,1346,1347,1348,1349,1350,1351,1352,1353,1354,198,1240,1355,1356,1357,1358,1359,198,1360,1361,1362,1363,1364,1365,1366,1247,1367,1368,1369,1370,1371,1104,1372,1373,1374,1375,1107,1108,1244,1245,1246,1247,1376,1377,1378,1379,1380,1381,1382,1373,1107,1383,1384,1385,1386,1387,1388,1389,1390,1391,1392,1393,1394,1395,1396,1397,1398,1380,1399,1400,1401,1402,1403,1404,1388,1405,198,198,1406,1407,1408,1409,965,1410,1411,1412,1413,1414,1415,1416,198,198,1417,965,1418,1411,1419,1413,1420,1181,1421,1422,1423,198,198,1424,1234,1425,1426,1427,1428,1429,1430,1431,1432,1433,1434,1435,1436,1437,1438,1437,1439,1006,1440,1441,1442,1443,1444,1445,1446,1447,1448,1449,1450,1445,1451,1247,915,1452,198,198,1453,1454,1455,1456,198,1457,198,1458,1459,1460,1461,198,1462,1459,1463,1461,198,1464,1459,1465,1461,198,1466,1467,1468,198,198,1469,1454,1455,1470,198,1471,198,1472,198,1473,1474,1475,198,1476,198,1477,1478,1479,198,1480,198,1477,1481,1479,198,1482,198,1477,1483,1479,198,1484,198,1485,1486,1487,1488,1489,1490,1491,1467,1468,198,198,1492,1493,1494,1495,198,1496,1497,1498,1499,1500,1501,1502,1503,1504,1505,1506,1507,1508,198,1509,1510,1511,1512,1513,1046,1514,1515,1046,198,1516,1517,1518,1519,1520,1521,1522,1523,1524,198,1525,1526,1527,1528,1529,1530,1531,198,1532,1533,1534,1535,1536,1537,198,1538,1539,1540,1541,1542,1543,1544,198,1545,1546,1547,1548,1549,1550,198,1551,1552,1553,198,1554,1555,1556,1557,1411,1558,1559,1560,198,1561,1021,1562,1563,1041,1025,198,1564,1565,1566,198,1567,1568,1569,1570,1571,1572,1573,1574,1396,1350,1575,1576,1577,1578,1579,1580,1581,1396,1582,1583,1396,1584,198,1585,1586,1587,1588,1411,1589,1389,1590,1591,1592,1413,1593,198,1594,1595,1596,1597,1598,1599,1600,1601,160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2274,2275,2276,2277,2275,2278,2279,2275,2280,1025,2281,198,198,2282,1884,1015,938,1018,941,942,2283,2284,2285,2286,2287,2288,1129,2289,2290,2291,1388,2292,1389,2293,2294,2295,1104,2296,2297,1580,1107,1108,1388,2298,198,2299,2300,2301,2302,2303,2304,198,2305,198,2306,2307,2308,1058],"contains_end_of_file","from __future__ import annotations","import contextlib","import hashlib","import importlib.util","import json","import os","import platform","import re","import shutil","import sqlite3","import stat","import subprocess","import sys","import tarfile","import uuid","import zipfile","from datetime import datetime, timezone","from pathlib import Path","from dataclasses import dataclass","from typing import Any, Callable, Iterator","from textwrap import dedent","try:"," import tomllib","except ModuleNotFoundError: # pragma: no cover - pyproject requires 3.11+"," tomllib = None # type: ignore[assignment]","EXCLUDED_DIR_NAMES = {"," \".sandbox\","," \".sandbox-bin\","," \".sandbox-secrets\","," \".tmp\","," \".venv\","," \"tmp\",","}","SIZE_REPORT_LIMIT = 10","LIVE_SQLITE_SUFFIXES = ("," \".sqlite-wal\","," \".sqlite-shm\","," \"-wal\","," \"-shm\",",")","def _make_sensitive_note(display_name: str) -> str:"," return ("," f\"This backup can contain {display_name} history, provider configuration, \""," \"login state, local hooks, and other sensitive environment data. Keep it \""," \"offline unless you have explicitly reviewed and approved another storage location.\""," )","@dataclass(frozen=True)","class EnvironmentProfile:"," name: str"," display_name: str"," default_home_dir: str"," env_home_var: str | None"," backup_prefix: str"," pre_restore_prefix: str"," default_backup_subdir: str"," important_paths: tuple[str, ...]"," config_file: str | None"," config_inspector: Callable[[Path], dict[str, Any]] | None"," commands: tuple[tuple[str, ...], ...]"," integration_module: str | None"," extra_excluded_dirs: tuple[str, ...] = ()","class BackupError(RuntimeError):"," \"\"\"Raised when a backup or restore cannot complete safely.\"\"\"","def utc_now_iso() -> str:"," return datetime.now(timezone.utc).replace(microsecond=0).isoformat()","def local_timestamp(prefix: str = \"codex-backup\") -> str:"," return f\"{prefix}-{datetime.now().strftime('%Y%m%d-%H%M%S')}\"","def resolve_home("," profile: EnvironmentProfile | None = None,"," home_override: str | os.PathLike[str] | None = None,",") -> Path:"," if profile is None:"," profile = CODEX_PROFILE"," if home_override:"," return Path(home_override).expanduser().resolve()"," if profile.env_home_var is not None:"," env_home = os.environ.get(profile.env_home_var)"," if env_home:"," return Path(env_home).expanduser().resolve()"," return (Path.home() / profile.default_home_dir).resolve()","def resolve_codex_home(codex_home: str | os.PathLike[str] | None = None) -> Path:"," return resolve_home(CODEX_PROFILE, codex_home)","def default_backup_root(profile: EnvironmentProfile | None = None) -> Path:"," home = Path.home()"," documents = home / \"Documents\""," if documents.exists() and not documents.is_dir():"," return (home / profile.default_backup_subdir).resolve()"," return (documents / profile.default_backup_subdir).resolve()","def default_backup_roots_for_discovery(profile: EnvironmentProfile | None = None) -> list[Path]:"," primary = default_backup_root(profile)"," fallback = (Path.home() / profile.default_backup_subdir).resolve()"," if fallback == primary:"," return [primary]"," return [primary, fallback]","def is_relative_to(child: Path, parent: Path) -> bool:"," try:"," child.resolve().relative_to(parent.resolve())"," return True"," except ValueError:"," return False","def normalize_relative(path: Path) -> str:"," return path.as_posix()","def is_excluded("," relative_path: Path,"," extra_excluded_dirs: frozenset[str] = frozenset(),",") -> bool:"," excluded = EXCLUDED_DIR_NAMES | extra_excluded_dirs"," parts = [part.lower() for part in relative_path.parts if part not in (\"\", \".\")]"," if any(part in excluded for part in parts):"," name = relative_path.name.lower()"," return name.endswith(LIVE_SQLITE_SUFFIXES)","def is_sqlite_database(path: Path) -> bool:"," return path.suffix.lower() == \".sqlite\"","def regular_file_skip_reason(path: Path) -> str | None:"," mode = path.lstat().st_mode"," if stat.S_ISLNK(mode):"," return \"symlink\""," if not stat.S_ISREG(mode):"," return \"not a regular file\""," return None","def sha256_file(path: Path) -> str:"," digest = hashlib.sha256()"," with path.open(\"rb\") as handle:"," for chunk in iter(lambda: handle.read(1024 * 1024), b\"\"):"," digest.update(chunk)"," return digest.hexdigest().upper()","def write_json(path: Path, data: Any) -> None:"," path.parent.mkdir(parents=True, exist_ok=True)"," path.write_text(json.dumps(data, indent=2, sort_keys=True) + \"\\n\", encoding=\"utf-8\")","def redact_text(text: str) -> str:"," patterns = ["," (r\"sk-[A-Za-z0-9_\\-]{12,}\", \"sk-\"),"," (r\"(api[_-]?key\\s*[:=]\\s*)[^\\s,;}]+\", r\"\\1\"),"," (r\"(authorization\\s*[:=]\\s*bearer\\s+)[^\\s,;}]+\", r\"\\1\"),"," (r\"(\\\"access_token\\\"\\s*:\\s*\\\")[^\\\"]+(\\\")\", r\"\\1\\2\"),"," (r\"(\\\"refresh_token\\\"\\s*:\\s*\\\")[^\\\"]+(\\\")\", r\"\\1\\2\"),"," ]"," redacted = text"," for pattern, replacement in patterns:"," redacted = re.sub(pattern, replacement, redacted, flags=re.IGNORECASE)"," return redacted","def run_command("," command: list[str],"," timeout: int = 20,"," env: dict[str, str] | None = None,"," *,"," include_output: bool = True,"," json_summary: bool = False,",") -> dict[str, Any]:"," path = env.get(\"PATH\") if env is not None else None"," if shutil.which(command[0], path=path) is None and Path(command[0]).name == command[0]:"," return {"," \"command\": command,"," \"status\": \"skipped\","," \"reason\": \"command_not_found\","," }"," completed = subprocess.run("," command,"," capture_output=True,"," text=True,"," timeout=timeout,"," check=False,"," env=env,"," )"," except subprocess.TimeoutExpired as exc:"," \"status\": \"timeout\","," \"timeout_seconds\": timeout,"," \"stdout\": redact_text(exc.stdout or \"\"),"," \"stderr\": redact_text(exc.stderr or \"\"),"," except OSError as exc:"," \"status\": \"error\","," \"error\": str(exc),"," result: dict[str, Any] = {"," \"command\": command,"," \"status\": \"ok\" if completed.returncode == 0 else \"failed\","," \"returncode\": completed.returncode,"," }"," stdout = completed.stdout.strip()"," stderr = completed.stderr.strip()"," if json_summary:"," result[\"stdout_summary\"] = summarize_json_output(stdout)"," result[\"output_redacted\"] = not include_output"," if include_output:"," result[\"stdout\"] = redact_text(stdout)"," result[\"stderr\"] = redact_text(stderr)"," else:"," result[\"stdout_bytes\"] = len(stdout.encode(\"utf-8\"))"," result[\"stderr_bytes\"] = len(stderr.encode(\"utf-8\"))"," return result","def summarize_json_output(text: str) -> dict[str, Any]:"," if not text:"," return {\"parse_status\": \"empty\"}"," data = json.loads(text)"," except json.JSONDecodeError:"," return {\"parse_status\": \"failed\", \"stdout_present\": True}"," if not isinstance(data, dict):"," return {\"parse_status\": \"ok\", \"json_type\": type(data).__name__}"," summary: dict[str, Any] = {\"parse_status\": \"ok\"}"," for key in ("," \"ok\","," \"status\","," \"installed\","," \"running\","," \"healthy\","," \"runtime_matches\","," \"needs_restart\","," \"pending_restart\","," \"config_matches\","," \"startup_hook\","," ):"," if key in data and isinstance(data[key], (bool, str, int, float, type(None))):"," summary[key] = data[key]"," \"provider\","," \"base_url\","," \"upstream_base\","," \"config_base_url\","," \"log\","," \"stdout\","," \"stderr\","," if key in data:"," summary[f\"{key}_present\"] = data[key] is not None"," health = data.get(\"health\")"," if isinstance(health, dict):"," summary[\"health\"] = {"," \"ok\": health.get(\"ok\"),"," \"service_tier_present\": health.get(\"service_tier\") is not None,"," \"upstream_base_present\": health.get(\"upstream_base\") is not None,"," \"runtime_id_present\": health.get(\"runtime_id\") is not None,"," checks = data.get(\"checks\")"," if isinstance(checks, list):"," safe_checks = []"," for check in checks:"," if isinstance(check, dict):"," safe_checks.append("," {"," \"name\": str(check.get(\"name\", \"\")),"," \"ok\": check.get(\"ok\"),"," }"," )"," summary[\"checks\"] = safe_checks"," return summary","def summarize_command_results(commands: dict[str, dict[str, Any]], *, run: bool) -> dict[str, Any]:"," failed: list[dict[str, Any]] = []"," skipped: list[dict[str, Any]] = []"," if not run:"," \"run\": False,"," \"ok\": True,"," \"total\": 0,"," \"failed\": failed,"," \"skipped\": [{\"name\": \"external_commands\", \"reason\": \"disabled\"}],"," for name, result in sorted(commands.items()):"," status = result.get(\"status\", \"unknown\")"," if status == \"skipped\":"," skipped.append("," {"," \"name\": name,"," \"reason\": result.get(\"reason\", \"skipped\"),"," }"," )"," continue"," if status != \"ok\":"," failed.append("," \"status\": status,"," \"returncode\": result.get(\"returncode\"),"," \"reason\": result.get(\"reason\") or result.get(\"error\"),"," return {"," \"run\": True,"," \"ok\": not failed,"," \"total\": len(commands),"," \"failed\": failed,"," \"skipped\": skipped,","def inspect_codex_config(codex_home: Path) -> dict[str, Any]:"," config_path = codex_home / \"config.toml\""," \"path\": \"config.toml\","," \"present\": config_path.exists(),"," if not config_path.exists():"," return result"," result[\"bytes\"] = config_path.stat().st_size"," if tomllib is None:"," result[\"parse_status\"] = \"skipped\""," result[\"reason\"] = \"tomllib_unavailable\""," data = tomllib.loads(config_path.read_text(encoding=\"utf-8\"))"," except Exception as exc: # tomllib exposes several parse errors."," result[\"parse_status\"] = \"failed\""," result[\"error\"] = str(exc)"," providers = data.get(\"model_providers\")"," active_provider = data.get(\"model_provider\")"," provider_summary: dict[str, Any] = {}"," if isinstance(providers, dict):"," for name, provider in providers.items():"," if isinstance(provider, dict):"," provider_summary[str(name)] = {"," \"base_url_present\": \"base_url\" in provider,"," \"env_key_present\": \"env_key\" in provider,"," \"service_tier_present\": \"service_tier\" in provider,"," \"wire_api_present\": \"wire_api\" in provider,"," result.update("," {"," \"parse_status\": \"ok\","," \"model_provider_present\": active_provider is not None,"," \"model_provider\": str(active_provider) if active_provider is not None else None,"," \"model_providers_present\": isinstance(providers, dict),"," \"model_provider_count\": len(providers) if isinstance(providers, dict) else 0,"," \"provider_fields\": provider_summary,"," \"hooks_enabled_present\": isinstance(data.get(\"features\"), dict)"," and \"codex_hooks\" in data.get(\"features\", {}),","inspect_config = inspect_codex_config","def inspect_claude_code_config(home: Path) -> dict[str, Any]:"," config_path = home / \"settings.json\""," \"path\": \"settings.json\","," data = json.loads(config_path.read_text(encoding=\"utf-8\"))"," except Exception as exc:"," result[\"error\"] = \"root is not an object\""," permissions = data.get(\"permissions\")"," hooks = data.get(\"hooks\")"," result.update({"," \"parse_status\": \"ok\","," \"permissions_present\": isinstance(permissions, dict),"," \"permissions_count\": len(permissions.get(\"allow\", [])) if isinstance(permissions, dict) else 0,"," \"env_present\": isinstance(data.get(\"env\"), dict),"," \"hooks_present\": isinstance(hooks, dict),"," \"hooks_count\": sum(len(v) for v in hooks.values() if isinstance(v, list)) if isinstance(hooks, dict) else 0,"," \"model\": data.get(\"model\"),"," \"theme\": data.get(\"theme\"),"," \"allowed_tools_present\": isinstance(data.get(\"allowedTools\"), list),"," })","CODEX_PROFILE = EnvironmentProfile("," name=\"codex\","," display_name=\"Codex\","," default_home_dir=\".codex\","," env_home_var=\"CODEX_HOME\","," backup_prefix=\"codex-backup\","," pre_restore_prefix=\"pre-restore-codex-backup\","," default_backup_subdir=\"CodexBackups\","," important_paths=("," \"auth.json\", \"hooks.json\", \"history.jsonl\", \"sessions\","," \"archived_sessions\", \"memories\", \"skills\", \"plugins\","," \"rules\", \"automations\", \"codex-fast-proxy-state\","," ),"," config_file=\"config.toml\","," config_inspector=inspect_codex_config,"," commands=((\"codex\", \"--version\"), (\"codex\", \"mcp\", \"list\")),"," integration_module=\"codex_fast_proxy\","," extra_excluded_dirs=(\"cache\", \"packages\", \"standalone\", \"node_modules\"),","CLAUDE_CODE_PROFILE = EnvironmentProfile("," name=\"claude-code\","," display_name=\"Claude Code\","," default_home_dir=\".claude\","," env_home_var=None,"," backup_prefix=\"claude-code-backup\","," pre_restore_prefix=\"pre-restore-claude-code-backup\","," default_backup_subdir=\"ClaudeCodeBackups\","," \"settings.json\", \"settings.local.json\", \"credentials.json\","," \"statsig\", \"projects\", \"memory\", \"todos\", \"plugins\","," \"keybindings.json\","," config_file=\"settings.json\","," config_inspector=inspect_claude_code_config,"," commands=((\"claude\", \"--version\"), (\"claude\", \"mcp\", \"list\")),"," integration_module=None,"," extra_excluded_dirs=(\"cache\",),","PROFILES: dict[str, EnvironmentProfile] = {"," \"codex\": CODEX_PROFILE,"," \"claude-code\": CLAUDE_CODE_PROFILE,","def count_tree("," path: Path,"," if not path.exists():"," return {\"present\": False, \"files\": 0, \"dirs\": 0}"," files = 0"," dirs = 0"," errors: list[dict[str, str]] = []"," def onerror(exc: OSError) -> None:"," errors.append(walk_error_entry(path, exc, method=\"walk\"))"," for root, dir_names, file_names in os.walk(path, onerror=onerror):"," rel_root = Path(root).relative_to(path)"," dir_names[:] = ["," name for name in dir_names"," if not is_excluded(rel_root / name, extra_excluded_dirs)"," ]"," dirs += len(dir_names)"," files += sum("," 1 for name in file_names"," return {\"present\": True, \"files\": files, \"dirs\": dirs, \"errors\": errors}","def _command_key(cmd: tuple[str, ...]) -> str:"," \"\"\"Derive a dict key from a command tuple, e.g. (\"codex\", \"--version\") -> \"codex_version\".\"\"\""," return \"_\".join(part.lstrip(\"-\") for part in cmd).replace(\"-\", \"_\")","def doctor_environment("," run_commands: bool = False,"," home = resolve_home(profile, home_override)"," core_ok = home.exists() and home.is_dir()"," config = profile.config_inspector(home) if profile.config_inspector is not None else {}"," report: dict[str, Any] = {"," \"ok\": core_ok,"," \"core_ok\": core_ok,"," \"created_at\": utc_now_iso(),"," \"home\": str(home),"," \"profile\": profile.name,"," \"platform\": {"," \"system\": platform.system(),"," \"release\": platform.release(),"," \"machine\": platform.machine(),"," \"python\": platform.python_version(),"," },"," \"sensitive_note\": _make_sensitive_note(profile.display_name),"," \"paths\": {},"," \"config\": config,"," \"commands\": {},"," extra_excluded = frozenset(profile.extra_excluded_dirs)"," for rel in profile.important_paths:"," target = home / rel"," if target.is_dir():"," report[\"paths\"][rel] = count_tree(target, extra_excluded)"," else:"," report[\"paths\"][rel] = {"," \"present\": target.exists(),"," \"bytes\": target.stat().st_size if target.exists() else 0,"," }"," path_scan_errors = ["," {\"path\": name, **error}"," for name, info in report[\"paths\"].items()"," for error in info.get(\"errors\", [])"," report[\"path_scan_ok\"] = not path_scan_errors"," report[\"path_scan_errors\"] = path_scan_errors"," if run_commands:"," command_env = os.environ.copy()"," if profile.env_home_var is not None:"," command_env[profile.env_home_var] = str(home)"," for cmd in profile.commands:"," report[\"commands\"][_command_key(cmd)] = run_command("," list(cmd), env=command_env"," if profile.integration_module is not None:"," module_name = profile.integration_module"," if importlib.util.find_spec(module_name) is not None:"," module_key = module_name.replace(\"-\", \"_\")"," report[\"commands\"][f\"{module_key}_status\"] = run_command("," [sys.executable, \"-m\", module_name, \"status\"],"," env=command_env,"," include_output=False,"," json_summary=True,"," report[\"commands\"][f\"{module_key}_doctor\"] = run_command("," [sys.executable, \"-m\", module_name, \"doctor\"],"," else:"," report[\"commands\"][module_name.replace(\"-\", \"_\")] = {"," \"status\": \"skipped\","," \"reason\": \"module_not_available\","," command_summary = summarize_command_results(report[\"commands\"], run=run_commands)"," report[\"command_summary\"] = command_summary"," report[\"command_ok\"] = command_summary[\"ok\"]"," report[\"checks\"] = {"," \"core\": report[\"core_ok\"],"," \"paths\": report[\"path_scan_ok\"],"," \"commands\": report[\"command_ok\"],"," report[\"ok\"] = all(report[\"checks\"].values())"," return report","def doctor_codex_environment("," codex_home: str | os.PathLike[str] | None = None,"," return doctor_environment(codex_home, profile=CODEX_PROFILE, run_commands=run_commands)","def error_relative_path(base: Path, raw_path: object) -> str:"," if not raw_path:"," return \".\""," path = Path(str(raw_path))"," return normalize_relative(path.resolve(strict=False).relative_to(base.resolve(strict=False)))"," except (OSError, ValueError):"," return str(path)","def walk_error_entry(base: Path, exc: OSError, *, method: str) -> dict[str, str]:"," \"relative_path\": error_relative_path(base, getattr(exc, \"filename\", None)),"," \"method\": method,"," \"error\": str(exc),","def iter_source_files("," home: Path,"," errors: list[dict[str, str]] | None = None,"," skipped: list[dict[str, str]] | None = None,",") -> Iterator[tuple[Path, Path]]:"," def excluded_subtree_stats(path: Path) -> tuple[int, int]:"," file_count = 0"," total_bytes = 0"," for walk_root, _, walk_files in os.walk(path):"," walk_root_path = Path(walk_root)"," for walk_file in walk_files:"," walk_path = walk_root_path / walk_file"," file_count += 1"," try:"," total_bytes += walk_path.stat().st_size"," except OSError:"," pass"," return file_count, total_bytes"," entry = walk_error_entry(home, exc, method=\"walk\")"," if errors is not None:"," errors.append(entry)"," return"," raise BackupError(entry[\"error\"])"," for root, dir_names, file_names in os.walk(home, onerror=onerror):"," root_path = Path(root)"," rel_root = root_path.relative_to(home)"," excluded_dirs = ["," name"," for name in dir_names"," if is_excluded(rel_root / name, extra_excluded_dirs)"," if skipped is not None:"," for excluded_dir in excluded_dirs:"," excluded_path = root_path / excluded_dir"," file_count, total_bytes = excluded_subtree_stats(excluded_path)"," skipped.append("," \"relative_path\": normalize_relative(rel_root / excluded_dir),"," \"reason\": \"excluded\","," \"file_count\": file_count,"," \"bytes\": total_bytes,"," for file_name in file_names:"," source = root_path / file_name"," relative = source.relative_to(home)"," if is_excluded(relative, extra_excluded_dirs):"," if skipped is not None:"," entry = {"," \"relative_path\": normalize_relative(relative),"," try:"," entry[\"bytes\"] = source.stat().st_size"," except OSError:"," pass"," skipped.append(entry)"," continue"," try:"," skip_reason = regular_file_skip_reason(source)"," except OSError as exc:"," entry = walk_error_entry(home, exc, method=\"stat\")"," entry[\"relative_path\"] = normalize_relative(relative)"," if errors is not None:"," errors.append(entry)"," continue"," raise BackupError(entry[\"error\"]) from exc"," if skip_reason is not None:"," skipped.append("," {"," \"relative_path\": normalize_relative(relative),"," \"reason\": skip_reason,"," }"," )"," yield source, relative","def backup_sqlite_database(source: Path, destination: Path) -> None:"," destination.parent.mkdir(parents=True, exist_ok=True)"," uri = source.resolve().as_uri() + \"?mode=ro\""," source_conn = sqlite3.connect(uri, uri=True, timeout=30.0)"," dest_conn = sqlite3.connect(str(destination), timeout=30.0)"," try:"," source_conn.backup(dest_conn)"," finally:"," dest_conn.close()"," finally:"," source_conn.close()","def sqlite_integrity_check(database: Path) -> dict[str, Any]:"," conn = sqlite3.connect(str(database), timeout=30.0)"," row = conn.execute(\"PRAGMA integrity_check\").fetchone()"," conn.close()"," return {\"path\": str(database), \"ok\": False, \"error\": str(exc)}"," value = row[0] if row else None"," return {\"path\": str(database), \"ok\": value == \"ok\", \"result\": value}","def write_environment_snapshot("," doctor_report: dict[str, Any],"," display_name: str = \"Codex\",",") -> None:"," lines = ["," f\"{display_name} environment snapshot\","," f\"Created: {doctor_report['created_at']}\","," f\"{display_name} home: {doctor_report['home']}\","," f\"Platform: {doctor_report['platform']['system']} {doctor_report['platform']['release']} {doctor_report['platform']['machine']}\","," f\"Python: {doctor_report['platform']['python']}\","," f\"Core ok: {doctor_report.get('core_ok')}\","," f\"Path scan ok: {doctor_report.get('path_scan_ok')}\","," f\"Command ok: {doctor_report.get('command_ok')}\","," \"\","," _make_sensitive_note(display_name),"," \"Important paths:\","," for name, info in doctor_report[\"paths\"].items():"," lines.append(f\"- {name}: present={info.get('present')}\")"," config = doctor_report.get(\"config\", {})"," lines.extend("," ["," \"\","," \"Config:\","," f\"- present={config.get('present')}\","," f\"- parse_status={config.get('parse_status')}\","," f\"- model_provider_present={config.get('model_provider_present')}\","," f\"- model_provider_count={config.get('model_provider_count')}\","," \"Secrets, auth payloads, and conversation contents are intentionally not printed here.\","," path.write_text(\"\\n\".join(lines) + \"\\n\", encoding=\"utf-8\")","def restore_kit_instructions(display_name: str = \"Codex\") -> str:"," return dedent("," f\"\"\""," {display_name} environment restore kit"," This folder contains a restore helper for people who do not want to type CLI commands."," Windows:"," 1. Close the {display_name} app that uses this environment."," 2. Double-click restore-environment.cmd."," 3. Confirm the prompt."," macOS:"," 2. Double-click restore-environment.command."," Linux:"," 2. Run restore-environment.sh from a terminal."," The restore helper creates a pre-restore backup before it overwrites the environment home directory."," \"\"\""," ).strip() + \"\\n\"","def restore_kit_markdown(display_name: str = \"Codex\") -> str:"," # {display_name} Environment Restore"," This backup includes a restore kit for users who do not want to type CLI commands."," ## Before Restoring"," - Close the {display_name} app that uses this environment."," - Keep this backup local unless you have reviewed its contents."," - The restore helper creates a pre-restore backup before overwriting the environment home directory."," ## Windows"," 1. Extract the backup archive if needed."," 2. Double-click `restore-environment.cmd`."," 3. Type `RESTORE` when prompted."," ## macOS"," 2. Open `restore-environment.command`."," ## Linux"," 2. Run `restore-environment.sh`."," ## Files"," - `RESTORE.md`: Markdown restore guide."," - `RESTORE_INSTRUCTIONS.txt`: Plain-text restore guide."," - `restore-environment.cmd`: Windows double-click restore entry."," - `restore-environment.ps1`: Windows PowerShell restore script."," - `restore-environment.command`: macOS restore entry."," - `restore-environment.sh`: Linux restore entry."," - `restore-standalone.py`: Self-contained restore implementation.","RESTORE_STANDALONE_PY = dedent("," r\"\"\""," #!/usr/bin/env python3"," from __future__ import annotations"," import argparse"," import hashlib"," import json"," import os"," import shutil"," import sqlite3"," import stat"," import sys"," import tarfile"," import zipfile"," from datetime import datetime"," from pathlib import Path"," from textwrap import dedent"," EXCLUDED_DIR_NAMES = {\".sandbox\", \".sandbox-bin\", \".sandbox-secrets\", \".tmp\", \".venv\", \"tmp\"}"," LIVE_SQLITE_SUFFIXES = (\".sqlite-wal\", \".sqlite-shm\", \"-wal\", \"-shm\")"," PROFILE_HOME_DEFAULTS = {"," \"codex\": \".codex\","," \"claude-code\": \".claude\","," PROFILE_EXTRA_EXCLUDED = {"," \"claude-code\": {\"cache\"},"," def resolve_target_home(target_home: str | None = None, profile: str | None = None) -> Path:"," if target_home:"," return Path(target_home).expanduser().resolve()"," if profile == \"codex\":"," env_home = os.environ.get(\"CODEX_HOME\")"," if env_home:"," return Path(env_home).expanduser().resolve()"," default_dir = PROFILE_HOME_DEFAULTS.get(profile or \"codex\", \".codex\")"," return (Path.home() / default_dir).resolve()"," def default_backup_root(profile: str | None = None) -> Path:"," subdir = \"ClaudeCodeBackups\" if profile == \"claude-code\" else \"CodexBackups\""," home = Path.home()"," documents = home / \"Documents\""," if documents.exists() and (not documents.is_dir() or not os.access(documents, os.W_OK)):"," return (home / subdir).resolve()"," return (documents / subdir).resolve()"," def is_excluded(relative_path: Path, profile: str = \"codex\") -> bool:"," excluded = EXCLUDED_DIR_NAMES | PROFILE_EXTRA_EXCLUDED.get(profile, set())"," parts = [part.lower() for part in relative_path.parts if part not in (\"\", \".\")]"," if any(part in excluded for part in parts):"," return True"," return relative_path.name.lower().endswith(LIVE_SQLITE_SUFFIXES)"," def regular_file_skip_reason(path: Path) -> str | None:"," mode = path.lstat().st_mode"," if stat.S_ISLNK(mode):"," return \"symlink\""," if not stat.S_ISREG(mode):"," return \"not a regular file\""," return None"," def sha256_file(path: Path) -> str:"," digest = hashlib.sha256()"," with path.open(\"rb\") as handle:"," for chunk in iter(lambda: handle.read(1024 * 1024), b\"\"):"," digest.update(chunk)"," return digest.hexdigest().upper()"," def write_json(path: Path, data) -> None:"," path.parent.mkdir(parents=True, exist_ok=True)"," path.write_text(json.dumps(data, indent=2, sort_keys=True) + \"\\n\", encoding=\"utf-8\")"," def error_relative_path(base: Path, raw_path) -> str:"," if not raw_path:"," return \".\""," path = Path(str(raw_path))"," return path.resolve(strict=False).relative_to(base.resolve(strict=False)).as_posix()"," except (OSError, ValueError):"," return str(path)"," def walk_error_entry(base: Path, exc: OSError, method: str) -> dict:"," \"relative_path\": error_relative_path(base, getattr(exc, \"filename\", None)),"," \"method\": method,"," def iter_source_files(source_root: Path, errors: list, skipped: list, profile: str = \"codex\"):"," def onerror(exc: OSError) -> None:"," errors.append(walk_error_entry(source_root, exc, \"walk\"))"," for root, dir_names, file_names in os.walk(source_root, onerror=onerror):"," root_path = Path(root)"," rel_root = root_path.relative_to(source_root)"," dir_names[:] = [name for name in dir_names if not is_excluded(rel_root / name, profile)]"," for file_name in file_names:"," source = root_path / file_name"," relative = source.relative_to(source_root)"," if is_excluded(relative, profile):"," skip_reason = regular_file_skip_reason(source)"," except OSError as exc:"," errors.append({"," \"relative_path\": relative.as_posix(),"," \"method\": \"stat\","," \"error\": str(exc),"," })"," if skip_reason is not None:"," skipped.append({\"relative_path\": relative.as_posix(), \"reason\": skip_reason})"," yield source, relative"," def backup_sqlite_database(source: Path, destination: Path) -> None:"," destination.parent.mkdir(parents=True, exist_ok=True)"," uri = source.resolve().as_uri() + \"?mode=ro\""," source_conn = sqlite3.connect(uri, uri=True, timeout=30.0)"," dest_conn = sqlite3.connect(str(destination), timeout=30.0)"," source_conn.backup(dest_conn)"," finally:"," dest_conn.close()"," source_conn.close()"," def create_backup(source_home: Path, backup_root: Path, prefix: str, profile: str = \"codex\") -> dict:"," backup_root.mkdir(parents=True, exist_ok=True)"," backup_dir = backup_root / f\"{prefix}-{datetime.now().strftime('%Y%m%d-%H%M%S')}\""," suffix = 1"," while backup_dir.exists():"," backup_dir = backup_root / f\"{prefix}-{datetime.now().strftime('%Y%m%d-%H%M%S')}-{suffix}\""," suffix += 1"," files_dir = backup_dir / \"files\""," files_dir.mkdir(parents=True)"," entries = []"," sqlite_checks = []"," errors = []"," skipped = []"," for source, relative in iter_source_files(source_home, errors, skipped, profile):"," destination = files_dir / relative"," if source.suffix.lower() == \".sqlite\":"," backup_sqlite_database(source, destination)"," conn = sqlite3.connect(str(destination), timeout=30.0)"," row = conn.execute(\"PRAGMA integrity_check\").fetchone()"," finally:"," conn.close()"," sqlite_checks.append({\"path\": str(destination), \"ok\": (row[0] if row else None) == \"ok\"})"," destination.parent.mkdir(parents=True, exist_ok=True)"," shutil.copy2(source, destination, follow_symlinks=False)"," entries.append({\"relative_path\": relative.as_posix(), \"sha256\": sha256_file(destination)})"," write_json(backup_dir / \"manifest.json\", {"," \"schema_version\": 1,"," \"created_at\": datetime.now().isoformat(),"," \"profile\": profile,"," \"home\": str(source_home),"," \"backup_name\": backup_dir.name,"," \"counts\": {"," \"files\": len(entries),"," \"sqlite_databases\": sum(1 for item in entries if item[\"relative_path\"].lower().endswith(\".sqlite\")),"," \"errors\": len(errors),"," },"," \"errors\": errors,"," \"skipped\": skipped,"," \"entries\": entries,"," })"," write_json(backup_dir / \"sqlite-integrity-check.json\", sqlite_checks)"," (backup_dir / \"backup-summary.txt\").write_text("," \"Pre-restore backup created by restore helper.\\n\", encoding=\"utf-8\""," write_restore_kit(backup_dir)"," archive_path = backup_dir.with_name(f\"{backup_dir.name}.tar.gz\")"," with tarfile.open(archive_path, \"w:gz\") as tar:"," tar.add(backup_dir, arcname=backup_dir.name)"," sha = sha256_file(archive_path)"," (archive_path.with_name(f\"{archive_path.name}.sha256\")).write_text("," f\"{sha} {archive_path.name}\\n\", encoding=\"utf-8\""," \"ok\": not errors and all(check.get(\"ok\") for check in sqlite_checks),"," \"backup_dir\": str(backup_dir),"," \"archive\": str(archive_path),"," \"archive_sha256\": sha,"," def restore_kit_markdown() -> str:"," return dedent('''"," # Environment Restore"," - Close the app that uses this environment."," ''').strip() + \"\\n\""," def restore_kit_instructions() -> str:"," Environment restore kit"," 1. Close the app that uses this environment."," def write_restore_kit(backup_dir: Path) -> None:"," script_source = Path(__file__).read_text(encoding=\"utf-8\")"," (backup_dir / \"RESTORE.md\").write_text(restore_kit_markdown(), encoding=\"utf-8\")"," (backup_dir / \"RESTORE_INSTRUCTIONS.txt\").write_text(restore_kit_instructions(), encoding=\"utf-8\")"," (backup_dir / \"restore-standalone.py\").write_text(script_source, encoding=\"utf-8\")"," (backup_dir / \"restore-environment.ps1\").write_text(dedent('''"," $ErrorActionPreference = 'Stop'"," $scriptRoot = Split-Path -Parent $MyInvocation.MyCommand.Path"," Write-Host 'Close the app that uses this environment before restoring.'"," $answer = Read-Host 'Type RESTORE to apply this backup'"," if ($answer -ne 'RESTORE') { exit 1 }"," $pythonCmd = $null"," foreach ($candidate in @('python3', 'python')) {"," if (-not (Get-Command $candidate -ErrorAction SilentlyContinue)) {"," try {"," $versionText = & $candidate -c \"import sys; print(f'{sys.version_info.major}.{sys.version_info.minor}')\" 2>$null"," if ($LASTEXITCODE -ne 0) {"," $version = [version]($versionText | Select-Object -First 1)"," if ($version -ge [version]'3.11') {"," $pythonCmd = $candidate"," break"," } catch {"," if (-not $pythonCmd) { throw 'Python 3.11+ is required to restore this backup.' }"," & $pythonCmd \"$scriptRoot\\\\restore-standalone.py\" --backup-dir $scriptRoot --apply --confirm"," ''').strip() + \"\\n\", encoding=\"utf-8\")"," (backup_dir / \"restore-environment.cmd\").write_text(dedent('''"," @echo off"," setlocal"," set \"SCRIPT_DIR=%~dp0\""," powershell -NoProfile -ExecutionPolicy Bypass -File \"%SCRIPT_DIR%restore-environment.ps1\""," shell_script = dedent('''"," #!/bin/sh"," set -eu"," script_dir=$(CDPATH= cd -- \"$(dirname -- \"$0\")\" && pwd)"," printf 'Close the app that uses this environment before restoring.\\n'"," printf 'Type RESTORE to apply this backup: '"," read answer"," if [ \"$answer\" != \"RESTORE\" ]; then"," exit 1"," fi"," python_cmd=${PYTHON:-}"," if [ -n \"$python_cmd\" ]; then"," \"$python_cmd\" -c 'import sys; raise SystemExit(0 if sys.version_info >= (3, 11) else 1)' >/dev/null 2>&1 || {"," echo 'Python 3.11+ is required to restore this backup.' >&2"," exit 1"," }"," else"," for candidate in python3 python; do"," if command -v \"$candidate\" >/dev/null 2>&1 && \"$candidate\" -c 'import sys; raise SystemExit(0 if sys.version_info >= (3, 11) else 1)' >/dev/null 2>&1; then"," python_cmd=\"$candidate\""," break"," fi"," done"," if [ -z \"$python_cmd\" ]; then"," fi"," \"$python_cmd\" \"$script_dir/restore-standalone.py\" --backup-dir \"$script_dir\" --apply --confirm"," command_path = backup_dir / \"restore-environment.command\""," sh_path = backup_dir / \"restore-environment.sh\""," command_path.write_text(shell_script, encoding=\"utf-8\")"," sh_path.write_text(shell_script, encoding=\"utf-8\")"," for path in (command_path, sh_path):"," path.chmod(0o755)"," except OSError:"," pass"," def restore_overlay(backup_dir: Path, target_home: Path, profile: str = \"codex\") -> dict:"," if not files_dir.is_dir():"," raise SystemExit(f\"Backup directory does not contain files/: {backup_dir}\")"," restored = 0"," for source in files_dir.rglob(\"*\"):"," if not source.is_file():"," relative = source.relative_to(files_dir)"," if is_excluded(relative, profile):"," skipped.append(relative.as_posix())"," destination = target_home / relative"," destination.parent.mkdir(parents=True, exist_ok=True)"," shutil.copy2(source, destination, follow_symlinks=False)"," restored += 1"," return {\"restored_files\": restored, \"skipped\": skipped}"," def main(argv: list[str] | None = None) -> int:"," parser = argparse.ArgumentParser(description=\"Restore an environment backup.\")"," parser.add_argument(\"--backup-dir\", required=True)"," parser.add_argument(\"--target-home\")"," parser.add_argument(\"--codex-home\", dest=\"target_home\", help=argparse.SUPPRESS)"," parser.add_argument(\"--backup-root\")"," parser.add_argument(\"--apply\", action=\"store_true\")"," parser.add_argument(\"--confirm\", action=\"store_true\")"," args = parser.parse_args(argv)"," backup_dir = Path(args.backup_dir).expanduser().resolve()"," manifest_path = backup_dir / \"manifest.json\""," if not manifest_path.exists():"," raise SystemExit(f\"Missing manifest.json in {backup_dir}\")"," manifest = json.loads(manifest_path.read_text(encoding=\"utf-8\"))"," profile = manifest.get(\"profile\", \"codex\")"," target_home = resolve_target_home(args.target_home, profile)"," backup_root = Path(args.backup_root).expanduser().resolve() if args.backup_root else default_backup_root(profile)"," print(json.dumps({"," \"dry_run\": not args.apply,"," \"target_home\": str(target_home),"," \"source_manifest\": {"," \"created_at\": manifest.get(\"created_at\"),"," \"backup_name\": manifest.get(\"backup_name\"),"," \"file_count\": manifest.get(\"counts\", {}).get(\"files\"),"," \"sqlite_databases\": manifest.get(\"counts\", {}).get(\"sqlite_databases\"),"," }, indent=2))"," if not args.apply:"," return 0"," if not args.confirm:"," raise SystemExit(\"Missing confirmation for apply restore.\")"," pre_prefix = \"pre-restore-claude-code-backup\" if profile == \"claude-code\" else \"pre-restore-codex-backup\""," pre_restore = None"," if target_home.exists():"," pre_restore = create_backup(target_home, backup_root, pre_prefix, profile=profile)"," if not pre_restore.get(\"ok\"):"," print(json.dumps({"," \"ok\": False,"," \"pre_restore_backup\": pre_restore,"," \"restore\": {"," \"restored_files\": 0,"," \"skipped\": [],"," \"errors\": [{"," \"error\": \"pre_restore_backup_failed\","," \"message\": \"Restore aborted because the current environment home could not be backed up completely.\","," }],"," },"," }, indent=2))"," return 2"," target_home.mkdir(parents=True, exist_ok=True)"," result = restore_overlay(backup_dir, target_home, profile)"," post = {"," \"pre_restore_backup\": pre_restore,"," \"restore\": result,"," print(json.dumps(post, indent=2))"," return 0"," if __name__ == \"__main__\":"," raise SystemExit(main())"," \"\"\"",").lstrip()","def write_restore_kit(backup_dir: Path, display_name: str = \"Codex\") -> dict[str, str]:"," restore_md = backup_dir / \"RESTORE.md\""," instructions = backup_dir / \"RESTORE_INSTRUCTIONS.txt\""," restore_py = backup_dir / \"restore-standalone.py\""," restore_ps1 = backup_dir / \"restore-environment.ps1\""," restore_cmd = backup_dir / \"restore-environment.cmd\""," restore_command = backup_dir / \"restore-environment.command\""," restore_sh = backup_dir / \"restore-environment.sh\""," restore_md.write_text(restore_kit_markdown(display_name), encoding=\"utf-8\")"," instructions.write_text(restore_kit_instructions(display_name), encoding=\"utf-8\")"," restore_py.write_text(RESTORE_STANDALONE_PY, encoding=\"utf-8\")"," close_msg = f\"Close the {display_name} app that uses this environment before restoring.\""," restore_ps1.write_text("," dedent("," \"\"\""," $ErrorActionPreference = 'Stop'"," $scriptRoot = Split-Path -Parent $MyInvocation.MyCommand.Path"," Write-Host '__CLOSE_MSG__'"," $answer = Read-Host 'Type RESTORE to apply this backup'"," if ($answer -ne 'RESTORE') { exit 1 }"," $pythonCmd = $null"," foreach ($candidate in @('python3', 'python')) {"," if (-not (Get-Command $candidate -ErrorAction SilentlyContinue)) {"," try {"," $versionText = & $candidate -c \"import sys; print(f'{sys.version_info.major}.{sys.version_info.minor}')\" 2>$null"," if ($LASTEXITCODE -ne 0) {"," continue"," $version = [version]($versionText | Select-Object -First 1)"," if ($version -ge [version]'3.11') {"," $pythonCmd = $candidate"," break"," } catch {"," if (-not $pythonCmd) { throw 'Python 3.11+ is required to restore this backup.' }"," & $pythonCmd \"$scriptRoot\\\\restore-standalone.py\" --backup-dir $scriptRoot --apply --confirm"," ).strip().replace(\"__CLOSE_MSG__\", close_msg)"," + \"\\n\","," encoding=\"utf-8\","," restore_cmd.write_text("," @echo off"," setlocal"," set \"SCRIPT_DIR=%~dp0\""," powershell -NoProfile -ExecutionPolicy Bypass -File \"%SCRIPT_DIR%restore-environment.ps1\""," ).strip()"," restore_command.write_text("," #!/bin/sh"," set -eu"," script_dir=$(CDPATH= cd -- \"$(dirname -- \"$0\")\" && pwd)"," printf '__CLOSE_MSG__\\n'"," printf 'Type RESTORE to apply this backup: '"," read answer"," if [ \"$answer\" != \"RESTORE\" ]; then"," exit 1"," python_cmd=${PYTHON:-}"," if [ -n \"$python_cmd\" ]; then"," \"$python_cmd\" -c 'import sys; raise SystemExit(0 if sys.version_info >= (3, 11) else 1)' >/dev/null 2>&1 || {"," echo 'Python 3.11+ is required to restore this backup.' >&2"," exit 1"," }"," else"," for candidate in python3 python; do"," if command -v \"$candidate\" >/dev/null 2>&1 && \"$candidate\" -c 'import sys; raise SystemExit(0 if sys.version_info >= (3, 11) else 1)' >/dev/null 2>&1; then"," python_cmd=\"$candidate\""," break"," fi"," done"," if [ -z \"$python_cmd\" ]; then"," fi"," \"$python_cmd\" \"$script_dir/restore-standalone.py\" --backup-dir \"$script_dir\" --apply --confirm"," restore_sh.write_text("," restore_command.read_text(encoding=\"utf-8\"),"," restore_command.chmod(0o755)"," except OSError:"," pass"," restore_sh.chmod(0o755)"," \"restore_md\": str(restore_md),"," \"instructions\": str(instructions),"," \"restore_py\": str(restore_py),"," \"restore_ps1\": str(restore_ps1),"," \"restore_cmd\": str(restore_cmd),"," \"restore_command\": str(restore_command),"," \"restore_sh\": str(restore_sh),","def create_archive(backup_dir: Path, archive_format: str) -> Path:"," if archive_format == \"tar.gz\":"," return archive_path"," if archive_format == \"zip\":"," archive_path = backup_dir.with_name(f\"{backup_dir.name}.zip\")"," with zipfile.ZipFile(archive_path, \"w\", compression=zipfile.ZIP_DEFLATED) as archive:"," for path in backup_dir.rglob(\"*\"):"," archive.write(path, path.relative_to(backup_dir.parent))"," raise BackupError(f\"Unsupported archive format: {archive_format}\")","def create_backup("," backup_root: str | os.PathLike[str] | None = None,"," archive_format: str = \"tar.gz\","," make_archive: bool = True,"," timestamp: str | None = None,"," run_doctor_commands: bool = False,"," home = resolve_home(profile, codex_home)"," if not home.exists() or not home.is_dir():"," raise BackupError("," f\"{profile.display_name} home does not exist or is not a directory: {home}\""," root = Path(backup_root).expanduser().resolve() if backup_root else default_backup_root(profile)"," if is_relative_to(root, home):"," f\"backup_root must not be inside {profile.display_name} home\""," root.mkdir(parents=True, exist_ok=True)"," backup_name = timestamp or local_timestamp(profile.backup_prefix)"," backup_dir = root / backup_name"," suffix = 1"," while backup_dir.exists():"," backup_dir = root / f\"{backup_name}-{suffix}\""," suffix += 1"," backup_name = backup_dir.name"," files_dir = backup_dir / \"files\""," files_dir.mkdir(parents=True)"," entries: list[dict[str, Any]] = []"," sqlite_checks: list[dict[str, Any]] = []"," skipped: list[dict[str, str]] = []"," for source, relative in iter_source_files(home, errors, extra_excluded, skipped):"," destination = files_dir / relative"," method = \"copy2\""," if is_sqlite_database(source):"," method = \"sqlite_backup\""," sqlite_checks.append(sqlite_integrity_check(destination))"," stat = destination.stat()"," entries.append("," \"relative_path\": normalize_relative(relative),"," \"kind\": \"file\","," \"bytes\": stat.st_size,"," \"sha256\": sha256_file(destination),"," \"method\": method,"," except Exception as exc:"," errors.append("," \"error\": str(exc),"," total_backup_bytes = sum(entry[\"bytes\"] for entry in entries)"," top_files_by_size = sorted("," ("," {"," \"relative_path\": entry[\"relative_path\"],"," \"bytes\": entry[\"bytes\"],"," for entry in entries"," ),"," key=lambda item: item[\"bytes\"],"," reverse=True,"," )[:SIZE_REPORT_LIMIT]"," directory_sizes: dict[str, int] = {}"," for entry in entries:"," rel_path = Path(entry[\"relative_path\"])"," for parent in rel_path.parents:"," key = \".\" if str(parent) == \".\" else normalize_relative(parent)"," directory_sizes[key] = directory_sizes.get(key, 0) + entry[\"bytes\"]"," top_directories_by_size = ["," {\"relative_path\": path, \"bytes\": size}"," for path, size in sorted(directory_sizes.items(), key=lambda item: item[1], reverse=True)[:SIZE_REPORT_LIMIT]"," excluded_skipped = [item for item in skipped if item.get(\"reason\") == \"excluded\"]"," excluded_entries = sum(int(item.get(\"file_count\", 1)) for item in excluded_skipped)"," excluded_bytes = sum(int(item.get(\"bytes\", 0)) for item in excluded_skipped)"," sensitive_note = _make_sensitive_note(profile.display_name)"," doctor_report = doctor_environment(home, profile=profile, run_commands=run_doctor_commands)"," manifest = {"," \"schema_version\": 1,"," \"backup_name\": backup_name,"," \"archive_format\": archive_format if make_archive else None,"," \"sensitive_note\": sensitive_note,"," \"platform\": doctor_report[\"platform\"],"," \"exclusions\": {"," \"directory_names\": sorted(EXCLUDED_DIR_NAMES | set(profile.extra_excluded_dirs)),"," \"live_sqlite_suffixes\": list(LIVE_SQLITE_SUFFIXES),"," \"entries\": entries,"," \"errors\": errors,"," \"counts\": {"," \"files\": len(entries),"," \"bytes\": total_backup_bytes,"," \"sqlite_databases\": sum(1 for entry in entries if entry[\"method\"] == \"sqlite_backup\"),"," \"errors\": len(errors),"," \"skipped\": len(skipped),"," \"size_report\": {"," \"top_files_by_size\": top_files_by_size,"," \"top_directories_by_size\": top_directories_by_size,"," \"excluded_entries\": excluded_entries,"," \"excluded_bytes\": excluded_bytes,"," write_json(backup_dir / \"manifest.json\", manifest)"," write_json(backup_dir / \"sqlite-integrity-check.json\", sqlite_checks)"," write_json(backup_dir / \"doctor-report.json\", doctor_report)"," write_environment_snapshot(backup_dir / \"environment-snapshot.txt\", doctor_report, profile.display_name)"," ok = not errors and all(check.get(\"ok\") for check in sqlite_checks)"," summary_lines = ["," f\"{profile.display_name} environment backup\","," f\"Backup: {backup_dir}\","," f\"{profile.display_name} home: {home}\","," f\"Files: {len(entries)}\","," f\"Expanded size (files only): {total_backup_bytes} bytes\","," f\"SQLite databases: {manifest['counts']['sqlite_databases']}\","," f\"Errors: {len(errors)}\","," f\"Excluded entries: {excluded_entries} ({excluded_bytes} bytes)\","," f\"Integrity: {'ok' if all(check.get('ok') for check in sqlite_checks) else 'failed'}\","," \"Restore kit: RESTORE.md, RESTORE_INSTRUCTIONS.txt, restore-environment.cmd, restore-environment.ps1, restore-environment.command, restore-environment.sh\","," sensitive_note,"," (backup_dir / \"backup-summary.txt\").write_text("," \"\\n\".join(summary_lines) + \"\\n\", encoding=\"utf-8\""," restore_kit = write_restore_kit(backup_dir, profile.display_name)"," archive_path = None"," sha256_path = None"," archive_sha256 = None"," if make_archive:"," archive_path = create_archive(backup_dir, archive_format)"," archive_sha256 = sha256_file(archive_path)"," sha256_path = archive_path.with_name(f\"{archive_path.name}.sha256\")"," sha256_path.write_text(f\"{archive_sha256} {archive_path.name}\\n\", encoding=\"utf-8\")"," \"ok\": ok,"," \"backup_dir\": str(backup_dir),"," \"archive\": str(archive_path) if archive_path else None,"," \"archive_sha256\": archive_sha256,"," \"sha256_file\": str(sha256_path) if sha256_path else None,"," \"manifest\": str(backup_dir / \"manifest.json\"),"," \"sqlite_integrity\": str(backup_dir / \"sqlite-integrity-check.json\"),"," \"doctor_report\": str(backup_dir / \"doctor-report.json\"),"," \"restore_kit\": restore_kit,"," \"counts\": manifest[\"counts\"],","def safe_extract_tar(archive_path: Path, destination: Path) -> None:"," destination_resolved = destination.resolve()"," with tarfile.open(archive_path, \"r:*\") as archive:"," for member in archive.getmembers():"," target = (destination / member.name).resolve()"," if not is_relative_to(target, destination_resolved):"," raise BackupError(f\"Archive member escapes extraction root: {member.name}\")"," if member.isdir():"," if not member.isfile():"," raise BackupError(f\"Unsupported archive member type: {member.name}\")"," target.mkdir(parents=True, exist_ok=True)"," target.parent.mkdir(parents=True, exist_ok=True)"," extracted = archive.extractfile(member)"," if extracted is None:"," raise BackupError(f\"Unable to extract archive member: {member.name}\")"," with extracted, target.open(\"wb\") as handle:"," shutil.copyfileobj(extracted, handle)","def validate_tar_members(archive_path: Path) -> dict[str, Any]:"," root = Path(\"/__archive_validation__\")"," target = (root / member.name).resolve()"," if not is_relative_to(target, root):"," return {"," \"archive\": str(archive_path),"," \"error\": f\"Archive member escapes extraction root: {member.name}\","," if not member.isdir() and not member.isfile():"," \"error\": f\"Unsupported archive member type: {member.name}\","," return {\"ok\": True, \"archive\": str(archive_path)}","def safe_extract_zip(archive_path: Path, destination: Path) -> None:"," with zipfile.ZipFile(archive_path) as archive:"," for member in archive.infolist():"," target = (destination / member.filename).resolve()"," raise BackupError(f\"Archive member escapes extraction root: {member.filename}\")"," mode = member.external_attr >> 16"," file_type = stat.S_IFMT(mode)"," if member.is_dir():"," if file_type and file_type != stat.S_IFREG:"," raise BackupError(f\"Unsupported archive member type: {member.filename}\")"," with archive.open(member, \"r\") as source, target.open(\"wb\") as handle:"," shutil.copyfileobj(source, handle)","def validate_zip_members(archive_path: Path) -> dict[str, Any]:"," target = (root / member.filename).resolve()"," \"error\": f\"Archive member escapes extraction root: {member.filename}\","," \"error\": f\"Unsupported archive member type: {member.filename}\",","def validate_archive_members(archive_path: Path) -> dict[str, Any]:"," if archive_path.suffix == \".zip\":"," return validate_zip_members(archive_path)"," return validate_tar_members(archive_path)"," return {\"ok\": False, \"archive\": str(archive_path), \"error\": str(exc)}","def locate_backup_dir(path: Path) -> Path:"," if (path / \"manifest.json\").exists() and (path / \"files\").is_dir():"," return path"," candidates = ["," candidate.parent"," for candidate in path.rglob(\"manifest.json\")"," if (candidate.parent / \"files\").is_dir()"," if not candidates:"," raise BackupError(f\"No backup manifest/files directory found in: {path}\")"," candidates.sort(key=lambda candidate: len(candidate.parts))"," return candidates[0]","@contextlib.contextmanager","def temporary_extract_dir(source: Path, work_root: Path | None = None) -> Iterator[Path]:"," candidates = [candidate for candidate in (work_root, source.parent, Path.cwd()) if candidate]"," roots: list[Path] = []"," for candidate in candidates:"," root = Path(candidate).expanduser().resolve()"," if root not in roots:"," roots.append(root)"," errors: list[str] = []"," temp_dir = None"," for root in roots:"," root.mkdir(parents=True, exist_ok=True)"," candidate = root / f\"restore-work-{uuid.uuid4().hex}\""," candidate.mkdir()"," temp_dir = candidate"," break"," except OSError as exc:"," errors.append(f\"{root}: {exc}\")"," if temp_dir is None:"," \"Unable to create a restore extraction directory. Tried: \" + \"; \".join(errors)"," yield temp_dir"," shutil.rmtree(temp_dir, ignore_errors=True)","def open_backup_source(source: Path, work_root: Path | None = None) -> Iterator[Path]:"," source = source.expanduser().resolve()"," if source.is_dir():"," yield locate_backup_dir(source)"," return"," if not source.exists():"," raise BackupError(f\"Backup source does not exist: {source}\")"," with temporary_extract_dir(source, work_root) as temp_dir:"," lower_name = source.name.lower()"," if lower_name.endswith((\".tar.gz\", \".tgz\", \".tar\")):"," safe_extract_tar(source, temp_dir)"," elif lower_name.endswith(\".zip\"):"," safe_extract_zip(source, temp_dir)"," raise BackupError(f\"Unsupported backup archive: {source}\")"," yield locate_backup_dir(temp_dir)","def restore_plan("," backup_dir: Path,"," target_home: Path,"," files = ["," path"," for path in files_dir.rglob(\"*\")"," if path.is_file() and not is_excluded(path.relative_to(files_dir), extra_excluded_dirs)"," total_bytes = sum(path.stat().st_size for path in files)"," \"target_home\": str(target_home),"," \"files\": len(files),"," \"bytes\": total_bytes,"," \"mode\": \"overlay\","," \"will_prune_existing_files\": False,"," \"requires_app_closed\": True,"," \"will_skip_excluded_paths\": sorted(EXCLUDED_DIR_NAMES | extra_excluded_dirs),","def copy_backup_files("," restored = 0"," skipped: list[str] = []"," for source in files_dir.rglob(\"*\"):"," if not source.is_file():"," relative = source.relative_to(files_dir)"," if is_excluded(relative, extra_excluded_dirs):"," skipped.append(normalize_relative(relative))"," destination = target_home / relative"," return {\"restored_files\": restored, \"skipped\": skipped, \"errors\": errors}","def restore_backup("," source: str | os.PathLike[str],"," apply: bool = False,"," confirm: bool = False,"," run_post_restore_commands: bool = False,"," source_path = Path(source).expanduser().resolve()"," source_is_dir = source_path.is_dir()"," with open_backup_source(source_path, root) as backup_dir:"," plan = restore_plan(backup_dir, home, extra_excluded)"," if source_is_dir:"," restore_kit = {"," \"restore_md\": str(backup_dir / \"RESTORE.md\"),"," \"instructions\": str(backup_dir / \"RESTORE_INSTRUCTIONS.txt\"),"," \"restore_cmd\": str(backup_dir / \"restore-environment.cmd\"),"," \"restore_command\": str(backup_dir / \"restore-environment.command\"),"," \"restore_sh\": str(backup_dir / \"restore-environment.sh\"),"," \"restore_ps1\": str(backup_dir / \"restore-environment.ps1\"),"," \"available_in_archive\": True,"," \"source_archive\": str(source_path),"," \"instructions\": \"Extract the archive and open RESTORE.md, or RESTORE_INSTRUCTIONS.txt as a plain-text fallback, to use the no-command restore helper.\","," result: dict[str, Any] = {"," \"dry_run\": not apply,"," \"plan\": plan,"," \"restore_kit\": restore_kit,"," \"sensitive_note\": _make_sensitive_note(profile.display_name),"," manifest_profile = manifest.get(\"profile\", \"codex\")"," if manifest_profile != profile.name:"," result[\"profile_mismatch\"] = {"," \"backup_profile\": manifest_profile,"," \"restore_profile\": profile.name,"," \"warning\": ("," f\"This backup was created with profile '{manifest_profile}' \""," f\"but restore is using profile '{profile.name}'. \""," \"The backup may be restored to the wrong home directory.\""," ),"," if not apply:"," result[\"message\"] = ("," f\"Dry run only. Close {profile.display_name} before restore, then rerun with --apply \""," \"and --i-understand-this-restores-sensitive-state.\""," return result"," if not confirm:"," raise BackupError("," \"Restore apply requires --i-understand-this-restores-sensitive-state\""," if home.exists():"," pre_restore = create_backup("," home,"," backup_root=root,"," profile=profile,"," archive_format=archive_format,"," timestamp=local_timestamp(profile.pre_restore_prefix),"," run_doctor_commands=False,"," result.update("," \"pre_restore_backup\": pre_restore,"," \"restore\": {"," \"restored_files\": 0,"," \"skipped\": [],"," \"errors\": ["," {"," \"error\": \"pre_restore_backup_failed\","," \"message\": f\"Restore aborted because the current {profile.display_name} home could not be backed up completely.\","," }"," ],"," },"," \"ok\": False,"," return result"," home.mkdir(parents=True, exist_ok=True)"," copy_result = copy_backup_files(backup_dir, home, extra_excluded)"," post_doctor = doctor_environment(home, profile=profile, run_commands=run_post_restore_commands)"," result.update("," \"pre_restore_backup\": pre_restore,"," \"restore\": copy_result,"," \"post_restore_doctor\": post_doctor,"," \"post_restore_doctor_mode\": \"full\""," if run_post_restore_commands"," else \"structural\","," \"post_restore_next_steps\": ("," f\"Reopen {profile.display_name} or start a fresh CLI session, then run a full doctor check \""," \"against the restored home.\""," if not run_post_restore_commands"," else None"," \"ok\": not copy_result[\"errors\"] and post_doctor[\"ok\"],","def count_files_under(path: Path) -> int:"," return sum(1 for candidate in path.rglob(\"*\") if candidate.is_file())","def read_json_file(path: Path) -> dict[str, Any] | list[Any] | None:"," return json.loads(path.read_text(encoding=\"utf-8\"))"," except Exception:","def backup_list_item(manifest: Path, data: dict[str, Any]) -> dict[str, Any]:"," counts = data.get(\"counts\") if isinstance(data.get(\"counts\"), dict) else {}"," entries = data.get(\"entries\") if isinstance(data.get(\"entries\"), list) else []"," schema_version = data.get(\"schema_version\")"," schema_label = schema_version if schema_version is not None else \"legacy\""," files_dir = manifest.parent / \"files\""," files = counts.get(\"files\")"," if files is None and entries:"," files = len(entries)"," if files is None and files_dir.is_dir():"," files = count_files_under(files_dir)"," if files is None:"," files = count_files_under(manifest.parent)"," sqlite_databases = counts.get(\"sqlite_databases\")"," if sqlite_databases is None and entries:"," sqlite_databases = sum(1 for entry in entries if entry.get(\"method\") == \"sqlite_backup\")"," if sqlite_databases is None and isinstance(data.get(\"sqlite_online_backup\"), list):"," sqlite_databases = len(data[\"sqlite_online_backup\"])"," errors = counts.get(\"errors\")"," if errors is None and isinstance(data.get(\"errors\"), list):"," errors = len(data[\"errors\"])"," if errors is None:"," errors = 0"," archive_candidates = ["," manifest.parent.with_name(f\"{manifest.parent.name}.tar.gz\"),"," manifest.parent.with_name(f\"{manifest.parent.name}.zip\"),"," archive_validation = ["," validate_archive_members(path)"," for path in archive_candidates"," if path.exists()"," sqlite_integrity = read_json_file(manifest.parent / \"sqlite-integrity-check.json\")"," sqlite_failed = ("," isinstance(sqlite_integrity, list)"," and any(not check.get(\"ok\") for check in sqlite_integrity if isinstance(check, dict))"," status = \"ok\" if schema_version == 1 else \"legacy_manifest\""," if schema_version == 1 and ("," errors > 0"," or sqlite_failed"," or any(not item.get(\"ok\") for item in archive_validation)"," status = \"failed\""," item: dict[str, Any] = {"," \"backup_dir\": str(manifest.parent),"," \"status\": status,"," \"schema_version\": schema_label,"," \"profile\": data.get(\"profile\", \"codex\"),"," \"created_at\": data.get(\"created_at\") or data.get(\"generated_at\"),"," \"files\": files,"," \"sqlite_databases\": sqlite_databases,"," \"archives\": [str(path) for path in archive_candidates if path.exists()],"," if archive_validation:"," item[\"archive_validation\"] = archive_validation"," if sqlite_failed:"," item[\"sqlite_integrity_ok\"] = False"," if status == \"legacy_manifest\":"," item[\"legacy_summary\"] = {"," \"generated_at\": data.get(\"generated_at\"),"," \"root_files\": len(data.get(\"included_root_files\", []))"," if isinstance(data.get(\"included_root_files\"), list)"," else None,"," \"directories\": len(data.get(\"included_directories\", []))"," if isinstance(data.get(\"included_directories\"), list)"," \"sqlite_online_backup\": len(data.get(\"sqlite_online_backup\", []))"," if isinstance(data.get(\"sqlite_online_backup\"), list)"," \"counts_estimated\": True,"," return item","def list_backups("," roots = [Path(backup_root).expanduser().resolve()] if backup_root else default_backup_roots_for_discovery(profile)"," root = roots[0]"," items: list[dict[str, Any]] = []"," seen: set[Path] = set()"," for candidate_root in roots:"," if not candidate_root.exists():"," for manifest in sorted(candidate_root.rglob(\"manifest.json\")):"," resolved_manifest = manifest.resolve()"," if resolved_manifest in seen:"," seen.add(resolved_manifest)"," data = json.loads(manifest.read_text(encoding=\"utf-8\"))"," except Exception as exc:"," items.append("," \"backup_dir\": str(manifest.parent),"," \"status\": \"unreadable\","," items.append(backup_list_item(manifest, data))"," def _sort_key(item: dict[str, Any]) -> tuple[str, str]:"," created_at = item.get(\"created_at\")"," created_key = created_at if isinstance(created_at, str) else (\"\" if created_at is None else str(created_at))"," backup_dir = item.get(\"backup_dir\")"," backup_dir_key = backup_dir if isinstance(backup_dir, str) else (\"\" if backup_dir is None else str(backup_dir))"," return (created_key, backup_dir_key)"," items.sort(key=_sort_key, reverse=True)"," result: dict[str, Any] = {\"ok\": True, \"backup_root\": str(root), \"backups\": items}"," if not backup_root and len(roots) > 1:"," result[\"discovery_roots\"] = [str(candidate) for candidate in roots]",[2310,2311,2312,2313,2314,2315,2316,2317,2318],{"_819":45,"_45":2330},{"_819":2320,"_160":859,"_865":2321,"_866":2322},{"_819":45,"_45":2329},{"_819":2320,"_160":859,"_865":2327,"_866":2328},{"_819":45,"_45":2326},{"_819":2320,"_160":859,"_865":2324,"_866":2325},{"_819":45,"_45":2323},{"_819":2320,"_160":859,"_865":2321,"_866":2322},{"_819":45,"_45":2319},"\n\n**Testing**\n* ✅ `python -m pytest -q`","repo_file_citation",624,708,"\n* Committed changes on the current branch: `7db7023` with message `Count pruned excluded directories in size report`. ",1531,1540,"\n* Updated summary output line to report the corrected excluded entry count. ",1489,1523,"\n* Updated backup size-report aggregation to compute `excluded_entries` from excluded file counts (using `file_count` when present, defaulting to 1 for single-file exclusions) and kept `excluded_bytes` summed from skipped excluded items. ","### Summary\n* Implemented excluded-directory accounting inside `iter_source_files` by detecting directories pruned from `dir_names`, walking those excluded subtrees, and recording aggregate `file_count` + `bytes` in `skipped` metadata (without reading file contents). This preserves restore behavior while fixing size-report undercounting for excluded directory trees. ",{"_91":322,"_41":83,"_95":322,"_2333":2334,"_2335":2336,"_2337":2338,"_131":-5,"_118":2339},[82],"input_items",[2355,2356,2357,2358],"external_post_config",{"_2340":2341,"_261":195,"_2342":301,"_272":-5,"_839":255,"_2343":-5,"_2344":2345,"_2346":832,"_2347":-5,"_2348":-5,"_2349":2350,"_2351":15,"_2352":57,"_2353":52,"_2354":15},"user_model_slug","slug",1779267256.342698,"installation_id",133926257,"pr_number","review_trigger","comment_id",3272472040,"comment_type","pr_write_guard_token","pending_pr_reaction_id","pending_comment_reaction_id",393442565,"comment_if_no_findings","comment_on_error","share_url","is_parallel_review",{"_91":426,"_95":322,"_421":2370},{"_308":309,"_310":2366,"_2367":315,"_2368":128,"_318":-5,"_91":2369},{"_91":2359,"_310":2363,"_160":859,"_2361":2364,"_2362":2365},{"_91":2359,"_310":2360,"_160":-5,"_2361":-5,"_2362":-5},"pull_request_comment","\n### 💡 Codex Review\n\nHere are some automated review suggestions for this pull request.\n\n**Reviewed commit:** `d6dd97b6f8`\n \n\n

ℹ️ About Codex in GitHub

","side","line","Comments in the same thread:\n\n**_{_{![P2 Badge](https://img.shields.io/badge/P2-yellow?style=flat)}} Count pruned excluded directories in size report**\n\n`excluded_entries`/`excluded_bytes` are derived from `skipped`, but this block only appends entries for excluded files that are still reached in `file_names`. In the same function, excluded directories are removed from `dir_names` before traversal, so files under newly excluded paths like `cache/`, `packages/`, `standalone/`, and `node_modules/` are never visited and therefore never counted. This makes the new size report systematically understate excluded data (often reporting `0` bytes) when exclusions happen at directory level, which defeats the purpose of surfacing size drivers.\n\nUseful? React with 👍 / 👎.","RIGHT",652,"### Motivation\n- Backups were including large rebuildable runtime/cache data silently, inflating expanded backup directories and making size drivers invisible to users. \n- The intent is to keep restore safety unchanged while making exclusions explicit and surfacing size information so users can choose compact vs forensic backups.\n\n### Description\n- Add a `SIZE_REPORT_LIMIT` constant and compute per-backup size metadata including `bytes` total, `top_files_by_size`, and `top_directories_by_size` during `create_backup` and write them into the manifest under `size_report` and `counts.bytes`. \n- Record excluded/skipped entries when `iter_source_files` omits files for exclusion by appending `{\n\n------\n[Codex Task](https://chatgpt.com/codex/cloud/tasks/task_e_6a0d727c0fe48333b696d871aab713ba)","base_ref","head_ref","pull_request_info",[2371],{"_819":45,"_45":2372},"@codex address that feedback. Please count files and bytes under pruned excluded directories in the size report without including file contents or changing restore safety behavior. 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