apply_patch: pure-addition chunk ignores its `@@` context and silently inserts at end of file, reporting Success
Open 💬 4 comments Opened Jul 2, 2026 by evanklem
What version of Codex CLI is running?
codex-cli 0.142.5
What subscription do you have?
Pro
Which model were you using?
N/A. Model independent.
What platform is your computer?
Linux 7.0.9-arch2-1 x86_64 unknown
What terminal emulator and version are you using (if applicable)?
Polypore 0.1.0 (AppImage), TERM=xterm-256color, no multiplexer.
Codex doctor report
{
"schemaVersion": 1,
"generatedAt": "1783019646s since unix epoch",
"overallStatus": "fail",
"codexVersion": "0.142.5",
"checks": {
"app_server.status": {
"id": "app_server.status",
"category": "app-server",
"status": "ok",
"summary": "background server is not running",
"details": {
"control socket": "/home/klemlitos/.codex/app-server-control/app-server-control.sock",
"daemon state dir": "/home/klemlitos/.codex/app-server-daemon",
"mode": "ephemeral",
"pid file": "/home/klemlitos/.codex/app-server-daemon/app-server.pid (missing)",
"settings": "/home/klemlitos/.codex/app-server-daemon/settings.json (missing)",
"status": "not running",
"update-loop pid file": "/home/klemlitos/.codex/app-server-daemon/app-server-updater.pid (missing)"
},
"remediation": null,
"durationMs": 0
},
"auth.credentials": {
"id": "auth.credentials",
"category": "auth",
"status": "ok",
"summary": "auth is configured",
"details": {
"auth file": "/home/klemlitos/.codex/auth.json",
"auth storage mode": "File",
"stored API key": "false",
"stored ChatGPT tokens": "true",
"stored agent identity": "false",
"stored auth mode": "chatgpt"
},
"remediation": null,
"durationMs": 0
},
"config.load": {
"id": "config.load",
"category": "config",
"status": "ok",
"summary": "config loaded",
"details": {
"CODEX_HOME": "/home/klemlitos/.codex",
"config.toml": "/home/klemlitos/.codex/config.toml",
"config.toml parse": "ok",
"cwd": "/home/klemlitos/Dev/opensourcecontribution/oscontribution",
"enabled feature flags": "shell_tool, unified_exec, shell_snapshot, terminal_resize_reflow, sqlite, hooks, enable_request_compression, multi_agent, apps, tool_search_always_defer_mcp_tools, tool_suggest, plugins, in_app_browser, browser_use, browser_use_full_cdp_access, browser_use_external, computer_use, plugin_sharing, image_generation, resize_all_images, skill_mcp_dependency_install, mentions_v2, steer, guardian_approval, goals, collaboration_modes, tool_call_mcp_elicitation, personality, fast_mode, tui_app_server, auto_compaction, remote_compaction_v2, workspace_dependencies",
"feature flag overrides": "none",
"feature flags enabled": "33",
"log dir": "/home/klemlitos/.codex/log",
"mcp servers": "0",
"model": "gpt-5.5",
"model provider": "openai",
"sqlite home": "/home/klemlitos/.codex"
},
"remediation": null,
"durationMs": 0
},
"git.environment": {
"id": "git.environment",
"category": "git",
"status": "ok",
"summary": "git version 2.54.0",
"details": {
"PATH git #1": "/usr/bin/git",
"PATH git entries": "1",
"git build options": "git version 2.54.0; cpu: x86_64; built from commit: 94f057755b7941b321fd11fec1b2e3ca5313a4e0; sizeof-long: 8; sizeof-size_t: 8; shell-path: /bin/sh; rust: enabled; gettext: enabled; libcurl: 8.19.0; OpenSSL: OpenSSL 3.6.2 7 Apr 2026; zlib-ng: 2.3.3; SHA-1: SHA1_DC; SHA-256: SHA256_BLK; default-ref-format: files; default-hash: sha1",
"git exec path": "/usr/lib/git-core",
"git version": "git version 2.54.0",
"repo detected": "false",
"selected git": "/usr/bin/git"
},
"remediation": null,
"durationMs": 45
},
"installation": {
"id": "installation",
"category": "install",
"status": "fail",
"summary": "npm install -g @openai/codex would update a different install",
"details": {
"PATH codex #1": "/home/klemlitos/.local/bin/codex",
"PATH codex #2": "/home/klemlitos/.local/bin/codex",
"PATH codex #3": "/home/klemlitos/.local/bin/codex",
"PATH codex entries": "3",
"current executable": "/home/klemlitos/.npm/_npx/c8ab89660c602c20/node_modules/@openai/codex-linux-x64/vendor/x86_64-unknown-linux-musl/bin/codex",
"install context": "npm (package /home/klemlitos/.npm/_npx/c8ab89660c602c20/node_modules/@openai/codex-linux-x64/vendor/x86_64-unknown-linux-musl, bin /home/klemlitos/.npm/_npx/c8ab89660c602c20/node_modules/@openai/codex-linux-x64/vendor/x86_64-unknown-linux-musl/bin, resources /home/klemlitos/.npm/_npx/c8ab89660c602c20/node_modules/@openai/codex-linux-x64/vendor/x86_64-unknown-linux-musl/codex-resources, path /home/klemlitos/.npm/_npx/c8ab89660c602c20/node_modules/@openai/codex-linux-x64/vendor/x86_64-unknown-linux-musl/codex-path)",
"managed by bun": "false",
"managed by npm": "true",
"managed package root": "/home/klemlitos/.npm/_npx/c8ab89660c602c20/node_modules/@openai/codex",
"npm package root": "/home/klemlitos/.npm-global/lib/node_modules/@openai/codex",
"running package root": "/home/klemlitos/.npm/_npx/c8ab89660c602c20/node_modules/@openai/codex"
},
"remediation": "Fix PATH or npm prefix so the running package root (/home/klemlitos/.npm/_npx/c8ab89660c602c20/node_modules/@openai/codex) matches the npm global package root (/home/klemlitos/.npm-global/lib/node_modules/@openai/codex).",
"durationMs": 61
},
"mcp.config": {
"id": "mcp.config",
"category": "mcp",
"status": "ok",
"summary": "no MCP servers configured",
"details": {},
"remediation": null,
"durationMs": 0
},
"network.env": {
"id": "network.env",
"category": "network",
"status": "ok",
"summary": "network-related environment looks readable",
"details": {
"SSL_CERT_FILE": "readable file /etc/ssl/certs/ca-certificates.crt",
"proxy env vars": "none"
},
"remediation": null,
"durationMs": 0
},
"network.provider_reachability": {
"id": "network.provider_reachability",
"category": "reachability",
"status": "ok",
"summary": "active provider endpoints are reachable over HTTP",
"details": {
"ChatGPT base URL": "https://chatgpt.com/backend-api/ reachable (HTTP 404)",
"reachability mode": "ChatGPT auth"
},
"remediation": null,
"durationMs": 151
},
"network.websocket_reachability": {
"id": "network.websocket_reachability",
"category": "websocket",
"status": "ok",
"summary": "Responses WebSocket handshake succeeded",
"details": {
"DNS": "2 IPv4, 2 IPv6, first IPv6",
"auth mode": "chatgpt",
"connect timeout": "15000 ms",
"endpoint": "wss://chatgpt.com/backend-api/<redacted>",
"handshake result": "HTTP 101 Switching Protocols",
"model provider": "openai",
"models etag present": "true",
"provider name": "OpenAI",
"proxy env vars": "none",
"reasoning header": "false",
"server model present": "false",
"supports websockets": "true",
"wire API": "responses"
},
"remediation": null,
"durationMs": 794
},
"runtime.provenance": {
"id": "runtime.provenance",
"category": "runtime",
"status": "ok",
"summary": "running npm on linux-x86_64",
"details": {
"commit": "unknown",
"current executable": "/home/klemlitos/.npm/_npx/c8ab89660c602c20/node_modules/@openai/codex-linux-x64/vendor/x86_64-unknown-linux-musl/bin/codex",
"install method": "npm (package /home/klemlitos/.npm/_npx/c8ab89660c602c20/node_modules/@openai/codex-linux-x64/vendor/x86_64-unknown-linux-musl, bin /home/klemlitos/.npm/_npx/c8ab89660c602c20/node_modules/@openai/codex-linux-x64/vendor/x86_64-unknown-linux-musl/bin, resources /home/klemlitos/.npm/_npx/c8ab89660c602c20/node_modules/@openai/codex-linux-x64/vendor/x86_64-unknown-linux-musl/codex-resources, path /home/klemlitos/.npm/_npx/c8ab89660c602c20/node_modules/@openai/codex-linux-x64/vendor/x86_64-unknown-linux-musl/codex-path)",
"platform": "linux-x86_64",
"version": "0.142.5"
},
"remediation": null,
"durationMs": 0
},
"runtime.search": {
"id": "runtime.search",
"category": "search",
"status": "ok",
"summary": "search is OK (bundled)",
"details": {
"search command": "/home/klemlitos/.npm/_npx/c8ab89660c602c20/node_modules/@openai/codex-linux-x64/vendor/x86_64-unknown-linux-musl/codex-path/rg",
"search command readiness": "file exists",
"search provider": "bundled"
},
"remediation": null,
"durationMs": 0
},
"sandbox.helpers": {
"id": "sandbox.helpers",
"category": "sandbox",
"status": "ok",
"summary": "sandbox configuration is readable",
"details": {
"approval policy": "OnRequest",
"codex-linux-sandbox helper": "/home/klemlitos/.codex/tmp/arg0/codex-arg0Quyqni/codex-linux-sandbox",
"execve wrapper helper": "/home/klemlitos/.codex/tmp/arg0/codex-arg0Quyqni/codex-execve-wrapper",
"filesystem sandbox": "restricted",
"network sandbox": "restricted"
},
"remediation": null,
"durationMs": 0
},
"state.paths": {
"id": "state.paths",
"category": "state",
"status": "ok",
"summary": "state paths and databases are inspectable",
"details": {
"CODEX_HOME": "/home/klemlitos/.codex (dir)",
"active rollout files": "162 files, 800612511 total bytes, 4942052 average bytes",
"archived rollout files": "0 files, 0 total bytes, 0 average bytes",
"goals DB": "/home/klemlitos/.codex/goals_1.sqlite (file)",
"goals DB integrity": "ok",
"log DB": "/home/klemlitos/.codex/logs_2.sqlite (file)",
"log DB integrity": "ok",
"log dir": "/home/klemlitos/.codex/log (dir)",
"memories DB": "/home/klemlitos/.codex/memories_1.sqlite (file)",
"memories DB integrity": "ok",
"sqlite home": "/home/klemlitos/.codex (dir)",
"state DB": "/home/klemlitos/.codex/state_5.sqlite (file)",
"state DB integrity": "ok"
},
"remediation": null,
"durationMs": 402
},
"state.rollout_db_parity": {
"id": "state.rollout_db_parity",
"category": "threads",
"status": "ok",
"summary": "rollout files and state DB thread inventory agree",
"details": {
"default model provider": "openai",
"rollout DB active files": "162",
"rollout DB active rows": "162",
"rollout DB archive mismatches": "0",
"rollout DB archived files": "0",
"rollout DB archived rows": "0",
"rollout DB duplicate DB paths": "0",
"rollout DB duplicate rollout thread ids": "0",
"rollout DB malformed file names": "0",
"rollout DB missing active rows": "0",
"rollout DB missing archived rows": "0",
"rollout DB model providers": "openai=162",
"rollout DB rows": "162",
"rollout DB scan cap reached": "false",
"rollout DB scan errors": "0",
"rollout DB sources": "cli=154, exec=4, subagent:thread_spawn=4",
"rollout DB stale rows": "0"
},
"remediation": null,
"durationMs": 4749
},
"system.environment": {
"id": "system.environment",
"category": "system",
"status": "ok",
"summary": "OS language en-US",
"details": {
"EDITOR": "set",
"LANG": "en_US.UTF-8",
"VISUAL": "not set",
"os": "Arch Linux Rolling Release [64-bit]",
"os language": "en-US",
"os type": "Arch Linux",
"os version": "Rolling Release"
},
"remediation": null,
"durationMs": 8
},
"terminal.env": {
"id": "terminal.env",
"category": "terminal",
"status": "ok",
"summary": "terminal metadata was detected",
"details": {
"COLORTERM": "truecolor",
"DISPLAY": "present",
"TERM": "xterm-256color",
"WAYLAND_DISPLAY": "present",
"color output": "disabled (stdout is not a terminal)",
"effective locale": "en_US.UTF-8",
"stderr is terminal": "false",
"stdin is terminal": "false",
"stdout is terminal": "false",
"terminal": "unknown",
"terminal size": "80x24"
},
"remediation": null,
"durationMs": 3
},
"terminal.title": {
"id": "terminal.title",
"category": "title",
"status": "ok",
"summary": "terminal title default",
"details": {
"terminal title activity": "true",
"terminal title items": "activity, project-name",
"terminal title project source": "cwd",
"terminal title project value": "oscontribution",
"terminal title source": "default"
},
"remediation": null,
"durationMs": 0
},
"updates.status": {
"id": "updates.status",
"category": "updates",
"status": "fail",
"summary": "update would target a different npm install",
"details": {
"cached latest version": "0.142.5",
"check for update on startup": "true",
"last checked at": "2026-07-02T18:46:31.255194535Z",
"latest version": "0.142.5",
"latest version status": "current version is not older",
"npm package root": "/home/klemlitos/.npm-global/lib/node_modules/@openai/codex",
"running package root": "/home/klemlitos/.npm/_npx/c8ab89660c602c20/node_modules/@openai/codex",
"update action": "npm install -g @openai/codex",
"version cache": "/home/klemlitos/.codex/version.json"
},
"remediation": "Fix PATH or npm prefix so the running package root (/home/klemlitos/.npm/_npx/c8ab89660c602c20/node_modules/@openai/codex) matches the npm global package root (/home/klemlitos/.npm-global/lib/node_modules/@openai/codex).",
"durationMs": 344
}
}
}What issue are you seeing?
When an *** Update File hunk contains a chunk that consists only of + (added) lines anchored by a @@ context marker, a pure insertion, with no surrounding context lines and no - lines apply_patch:
- successfully locates the
@@context line in the file, - then discards that position and appends the new lines at the end of the file instead,
- and reports
Success. Updated the following files: M <file>with exit code 0.
The inserted code lands in a different scope than the patch requested (e.g. inside the last class in the file instead of the class named in the @@ line). Since the file still parses, the misplaced method can go unnoticed.
If the @@ line doesn't exist in the file, apply_patch correctly fails with Failed to find context ... so the anchor is validated, just not used.
What steps can reproduce the bug?
In a normal session, this triggers whenever the model emits a pure-addition chunk (an @@ anchor followed by only + lines) e.g. when asked to add a method to a named class. Since whether the model repeats context lines is nondeterministic per turn, the steps below invoke the apply_patch applet directly via --codex-run-as-apply-patch, which is the same entry point codex core uses when the model calls apply_patch (arg0/src/lib.rs, CODEX_CORE_APPLY_PATCH_ARG1), with a fixed payload:
cd "$(mktemp -d)"
cat > sample.py <<'PYEOF'
class Alpha:
def method_a(self):
return 1
class Beta:
def method_b(self):
return 2
class Gamma:
def method_c(self):
return 3
PYEOF
codex --codex-run-as-apply-patch "$(cat <<'EOF'
*** Begin Patch
*** Update File: sample.py
@@ class Alpha:
+ def method_new(self):
+ return 99
*** End Patch
EOF
)"
cat sample.pyObserved exit code 0, and method_new lands inside Gamma, not Alpha:
Success. Updated the following files:
M sample.pyclass Alpha:
def method_a(self):
return 1
class Beta:
def method_b(self):
return 2
class Gamma:
def method_c(self):
return 3
def method_new(self):
return 99What is the expected behavior?
Either of:
- The added lines are inserted immediately after the located
@@ class Alpha:context line, matching how every other chunk type respects the seek position after a context match, or - If pure-addition chunks are intentionally unsupported, apply_patch rejects the chunk with an error instead of applying it at the wrong location.
Additional information
Root cause is in codex-rs/apply-patch/src/lib.rs, compute_replacements():
- The
@@context is found viaseek_sequence, andline_indexis advanced to just past it (~lines 727–740). - The next branch handles empty
old_linesby unconditionally appending at EOF, never readingline_index:
if chunk.old_lines.is_empty() {
// Pure addition (no old lines). We'll add them at the end or just
// before the final empty line if one exists.
let insertion_idx = if original_lines.last().is_some_and(String::is_empty) {
original_lines.len() - 1
} else {
original_lines.len()
};
replacements.push((insertion_idx, 0, chunk.new_lines.clone()));
continue;
}The EOF fallback is only correct for the anchorless pure-addition case (no @@ at all). When chunk.change_context is Some(..) and the seek succeeded, the insertion should use line_index:
let insertion_idx = if chunk.change_context.is_some() {
line_index
} else if original_lines.last().is_some_and(String::is_empty) {
original_lines.len() - 1
} else {
original_lines.len()
};The parser explicitly allows this chunk shape (UpdateFileChunk { change_context: Some(..), old_lines: vec![], .. } — parser.rs doc comment: "old_lines must occur strictly after change_context"). This chunk shape is emitted whenever the model adds a method/function to a named scope without repeating context lines.
Distinct from #30505 (indentation corruption on fuzzy match).
This issue has 4 comments on GitHub. Read the full discussion on GitHub ↗