AgentDetox

Protection for what AI coding agents remember and obey. AgentDetox watches an agent's memory, instruction and rules files, skills and config: it checks what the agent writes there, notices what changes behind its back, and puts things back.

Status: preview. Claude Code is supported. Codex and Cursor hooks are experimental, and OpenClaw gets tamper detection only. Developed on macOS; on Windows the tests run in CI, but it has not yet been used on a real machine. Where it is going: ROADMAP.md. Features under [Unreleased] in the changelog are available from main; they may not yet be in the PyPI release.

Agents learn from web pages, files, emails and tool output, and some of it is written into memory or rules that every later session trusts. One poisoned write can steer an agent for weeks, as Cisco's persistent-memory compromise of Claude Code (April 2026) and MemGhost (arXiv 2607.05189, July 2026) showed. Today's models refuse much of the obvious injected text they read. What they cannot see is a file changed behind their back, by a dependency's install script or another program, which they then load as your instructions; and smaller models still save planted text when asked to remember "the setup steps".

See it

agentdetox demo

In a throwaway folder, with nothing else read or changed, the demo shows an agent trying to save a planted instruction to its memory (blocked), a dependency's install script slipping the same instruction into CLAUDE.md (reported as soon as the shell tool finishes, with a review id), and the file being restored. It runs the real hooks, so it doubles as a self-test.

Install

uv tool install agentdetox                # or: pipx install agentdetox

To run the latest code from main instead: uv tool install --force git+https://github.com/chriswu727/agentdetox.

Then install the Claude Code plugin, from inside Claude Code:

/plugin install agentdetox --marketplace chriswu727/agentdetox

or add the same hooks to your settings directly:

agentdetox install claude-code --apply    # registers hooks in ~/.claude/settings.json, backed up first

Restart Claude Code to load the hooks. Use one route, not both: install declines when the plugin is enabled, and agentdetox doctor warns if the hooks are registered twice. The plugin runs the agentdetox you installed; without one it runs its own release through uvx, and with neither it says so at session start instead of failing on every tool call.

A tool install keeps AgentDetox in an environment of its own; pip install agentdetox works too. If you move Claude Code's folder with CLAUDE_CONFIG_DIR, AgentDetox follows it. The first session scans what is already there before recording recovery checkpoints; agentdetox agent scan does the same at any time.

What it does in Claude Code

• Before a write to memory, CLAUDE.md, rules, skills or config (through Write, Edit or a shell command such as a redirect, tee, sed -i, cp, mv or rm), the new content is checked. Planted instructions are denied, with the reason sent to the agent. If the flagged text is something you typed or pasted yourself, you are asked instead (hidden text is still denied, since you could not see what you pasted). An agent changing its own hooks, MCP servers, permissions, environment variables or helper commands (apiKeyHelper and the like) needs your approval, and the prompt says exactly what is added or removed. Setting an AGENTDETOX_* variable through the agent's settings is denied.
• After the write, the observed version and available attribution evidence are recorded. A recovery checkpoint advances when the write passes the checks. This is separate from a version you explicitly accept in review.
• After a shell tool finishes or fails, compare the current project's context, its auto memory, and shared regular Claude context files with the versions captured before the tool. New, removed or changed files enter review immediately, with a short terminal notice. Config counters do not produce changes; security-relevant settings do. The record says the change happened during the tool, not which process authored it. If a separate Write/Edit hook already recorded the final version, it keeps that observed writer. A permission rule for the command being run, which Claude Code saves when you approve the command and choose not to be asked again, is recorded without a notice. Installations from 0.3 need updated hook registration (install claude-code --apply, or update the plugin); agentdetox doctor says when.
• At session start, files changed outside the agent since the last session are compared with the snapshot. Suspicious content is reported to the agent, which is told not to follow it and to tell you, with the command that restores each file; this repeats until you review it. Anything new that would run on your machine, other than AgentDetox's own, is mentioned once instead, worded as a question rather than an alarm: a hook or hook script, a helper or status line command, an MCP server, a plugin or marketplace, or an environment variable that loads code or redirects traffic (NODE_OPTIONS, *_BASE_URL, proxies and the like). If you added it yourself (claude mcp add, /plugin install), there is nothing to do; it stays in agentdetox review until you accept or dismiss it. Other edits that look benign, such as a new permission or an ordinary variable, do not interrupt; they are listed in agentdetox review as made outside the agent.

Where memory came from. A memory write that is mostly copied from web pages, MCP data, command output or files the agent just read asks for approval, unless you asked the agent to remember it. This is how text planted in an email or page usually reaches memory. Text the model rewrites in its own words is not caught this way.

What the rules look for is what a benign memory almost never asks for: running code fetched from the network, reverse shells, loosening the agent's own approvals or sandbox, reading credentials, acting silently, standing orders to fetch a URL every session, hidden text, and injection phrasing. Memory that points package installs at a registry other than the default ones and the big public mirrors asks rather than blocks, since teams do run private registries. English and Chinese.

Cleaning up. agentdetox review lists changes needing attention, with a C id for each change. agentdetox review C42 shows the diff, observed writer, attribution evidence and individual F finding ids. agentdetox restore C42 previews the recovery; add --apply to restore the version before that change. The current file is backed up in ~/.agentdetox/quarantine before replacement. Accept and restore refuse if the file has changed since that record; for a settings file, accept compares only the security-relevant settings, since Claude Code rewrites its own config at every start. agentdetox agent restore <file> restores the recovery checkpoint through the same journalled recovery. Recovery rescans the target version, warns about residual rule findings and keeps them pending. Recovery restores a whole version; it does not certify that the file is safe or preserve benign additions made within the change being undone. For a setting added outside the agent, removing it with the tool that added it (claude mcp remove, /plugin uninstall) is safer than restoring the whole settings file.

A missing or damaged metadata store is reported instead of silently rebuilt. Keep a backup of the whole store, including objects/. 0.4 upgrades the metadata format (from 1 in 0.3.x to 3) on its first write and keeps the old database beside it as ~/.agentdetox/state.v1.sqlite3. 0.3.x refuses the upgraded store; to go back, reinstall 0.3.x and put that copy back as state.sqlite3 (changes recorded since the upgrade are lost). agentdetox doctor shows the format in use. agentdetox agent snapshot --reset explicitly resets recovery checkpoints; it does not erase history or make a corrupt database safe to use.

Day to day

agentdetox status                         # health and pending reviews
agentdetox review                         # pending changes grouped by file
agentdetox review --interactive           # browse this project and confirm actions in a terminal
agentdetox review --interactive --global  # include shared user rules and configuration
agentdetox review --project . --since 7d   # this project and its Claude auto memory
agentdetox review --all --page 2          # page through older file groups
agentdetox review --file CLAUDE.md --all --group-by change # one file's history
agentdetox review --search permissions    # match a path or finding
agentdetox review C42                     # diff, evidence, and findings
agentdetox review accept C42              # accept only this exact file version
agentdetox review dismiss F7              # dismiss one finding; no permanent exception
agentdetox restore C42                    # preview; add --apply to restore
agentdetox review --since 7d               # recent context changes, including quiet activity
agentdetox log                            # all recorded changes
agentdetox blame ~/.claude/CLAUDE.md      # per-line attribution evidence
agentdetox events                         # hook decisions and health events
agentdetox doctor                         # verify effective hooks and store health
agentdetox export --format jsonl          # export change records
agentdetox history prune --older-than 90d # preview retention; add --apply to remove

Review lists support --page-size 1..200, --page, --group-by file|change, --file, --search, and --project. Counts describe the entire filtered selection, not just the current page. A project filter includes files under that project and its Claude auto-memory directory; shared user-level rules remain in the unfiltered view. Historical records require no migration. Interactive review defaults to the current project; --global includes shared user rules and configuration. It asks before accepting or applying recovery. It requires a terminal; scripts use explicit id-based commands. Review JSON is a page object with rows, totals, state/operation counts and pagination metadata.

The ledger separates the observed writer (an agent tool, external change or recovery) from content attribution. A match to your message or a tool result is text evidence, not proof of who authored it. Added lines are compared separately, so user wording and model additions in the same write receive different labels. Unmatched text is unknown; older migrated records retain a legacy-inference label. blame marks content predating the ledger as "earlier" and unseen edits as "unrecorded". Paraphrases and shell-command authorship remain unresolved.

Accepting C42 applies only to that exact version. Dismissing F7 leaves the recovery checkpoint and file unchanged. Neither adds a source to the allowlist. The advanced agentdetox allow <id> command still grants a persistent exception across checks, scans and future versions; agentdetox allow --list and --remove inspect and undo it.

Pending findings, explicitly accepted versions and each file's latest record survive history pruning. Unreferenced content objects are removed by the daily GC, or agentdetox agent gc. Quarantine backups and legacy migration files are never automatically deleted.

Settings live in ~/.agentdetox/config.toml (agentdetox config shows them). Each check is ask, record (the write goes through and is logged) or off; agents without an ask prompt record instead of asking. An AGENTDETOX_<KEY> environment variable overrides the file.

The settings, the allowlist and the snapshots are guarded like the agent's own config: an agent writing under ~/.agentdetox, deleting it, or running agentdetox allow, config <key> <value>, install, uninstall, agent snapshot, review mutations or recovery needs your approval, or an injected instruction could switch a check off or allow itself.

Hooks fail open: if AgentDetox itself errors, the agent's action proceeds, and an unresolved failure remains visible in doctor and status. After investigating, acknowledge its event id with agentdetox health acknowledge <event-id>. A missing optional model is an inactive feature, not a protection failure. Interrupted recoveries show their backup location in doctor; after inspection, health acknowledge-recovery <id> verifies the file matches one side of that recovery before acknowledging it. SQLite fallback errors use health acknowledge fallback. disableAllHooks is also checked. If an attacker deletes the hooks, the session-start check cannot run; agentdetox agent verify (by hand or in CI) still reports the removal.

What it does not catch

• Detection is not a security boundary. An adaptive attacker who knows these rules can evade them, and a plausible-looking false fact with nothing to contradict passes.
• Planted text the model rewrites in its own words before saving it, unless a rule still matches.
• Changes outside the observed shell interval remain visible at the next session or before the next observed edit. Background writes after a shell tool returns are outside that interval.
• The ledger knows what the hooks saw. A change the agent makes with a shell command is recorded as made outside the agent, and text it copied in its own words as the agent's.
• The check before a shell command reads the command, it does not run it. It follows redirects, tee, sed -i, perl -i, cp, mv, rm (including a whole folder that holds context files), a copy into a folder (cp x/CLAUDE.md ., cp -t .claude …, cp -r), git checkout/restore (also of ., and with git -C dir), curl -o and wget -O (also in bundles such as -sSLo), inline python -c/node -e code that names a context file, bash -c (also bash -lc) and eval, wrappers such as sudo -u root, env -C dir or xargs -I {}, and a cd or variable set earlier in the same command. A script file, a path built at run time (find … -exec), a folder copied to a place that holds no context yet, or an archive being unpacked is not stopped beforehand; the check right after the command finds the change and, if the new content is flagged, tells the agent not to follow it.
• Writes made by MCP tools are not checked when they happen; the next session's comparison finds them.
• CLAUDE.md files in subfolders are checked when the agent writes them, but changes made to them outside the agent are not looked for.
• The guard on AgentDetox's own settings recognises plain commands and file writes. An agent that can run arbitrary code can still change them (a script that edits ~/.agentdetox is not inspected), and nothing stops a person or process outside the agent.
• Settings added outside the agent are mentioned once. If nobody acts on that notice, the setting stays and is only listed in agentdetox review. A project opened for the first time is not reported for the hooks and MCP servers it brings; Claude Code asks you to trust it.
• A shell command that adds a permission rule for itself (Bash(python:*) while running a Python script) looks the same as Claude Code saving your approval, and is recorded without a notice.
• In .claude/hooks, only scripts are watched (a script extension, #!, or the executable bit), not packages installed beside them (node_modules, .venv). A data file or package that a hook script loads is not.
• Routine changes outside the agent, such as a git checkout or formatter touching CLAUDE.md or a permission saved for a tool other than Bash, each add an item to agentdetox review. There is no bulk accept yet; once the file has changed again, an older item is cleared by dismissing its findings one at a time.
• restore C42 refuses once the file has changed again for any reason. agent restore then puts back the latest checkpoint, which already includes a settings change that was mentioned once.
• On Windows the shell checks understand Git Bash commands (/c/... paths, agentdetox.exe), not PowerShell or cmd.exe syntax.

Other agents

Codex and Cursor cannot ask mid-task: checks set to ask record instead, and changes to the agent's own hooks, MCP servers or permissions are blocked. The provenance check needs Claude Code's session transcript.

Contradiction detection (experimental)

Optional: uv tool install 'agentdetox[nli]', then agentdetox fetch-models. A memory write that contradicts what the agent already knows is a common sign of a fabricated fact. This uses a multilingual NLI model (mDeBERTa-v3, about 560 MB) and records instead of asking: after a write, the hook hands the check to a background model server and returns (about 0.1 s), and conflicts are logged (agentdetox events) and attached to the matching version in review. The server loads the model on first use (about 1 GB of memory) and exits after 30 minutes without work; agentdetox daemon status shows it. On real memory the model still misreads fragments of notes as contradicting each other, which is why it does not ask; agentdetox config contradiction ask makes it ask. Windows has no model server yet: each related write starts a background worker that loads the model (about 6 s). The roadmap replaces this model with an LLM judge. Measurements: bench/MEMORY_BENCHMARK.md.

Also: scanning a RAG knowledge base

pip install 'agentdetox[st]'                # drop [st] for a numpy-only install
agentdetox scan ./knowledge_base            # directory of .txt/.md/.html, or a .jsonl export
agentdetox trace kb.jsonl -q "Who founded Acme?" -a "Bob Smith"

Try it on the bundled example: agentdetox scan examples/kb.

scan exits with status 1 when any finding is at least --fail-on severity (default high), so it can gate ingestion in CI. A similarity clique on its own is reported as medium, because legitimately repetitive content (versioned docs, templated pages) also forms cliques; it becomes high only for members that also open with a question or carry injection markers. Use --fail-on medium if you want paraphrase-only poisoning to block ingestion too.

poison-cluster implements CleanBase (Jin et al., arXiv 2605.00460): a k-nearest-neighbour cosine-similarity graph (k=10), edges kept above mu + 2.5 sigma of a 50% edge sample, and every passage in a clique of 3 or more flagged; exact duplicates are collapsed first. trace takes a question and the wrong answer your system gave, ranks the top 4 x top-k passages by the mean z-score of similarity to the question, similarity to the wrong answer and whether the passage contains the answer, and splits them with 1-D 2-means. It is a cheap approximation of RAGOrigin (Zhang et al., IEEE S&P 2026); treat its output as a ranked lead list.

Limits: poison-cluster cannot see an attacker who plants only one or two passages per target question or makes them deliberately dissimilar, and needs a few hundred passages to estimate its threshold; injection-phrase will flag security documentation that quotes attacks; brute-force kNN is fine for tens of thousands of passages, not millions. Measurements against PoisonedRAG and other scanners: bench/KB_BENCHMARK.md.

Development

./scripts/check.sh       # lint, type checks and tests: what every change must pass
./scripts/update.sh      # the checks, then update the installed agentdetox, then `agentdetox doctor`

CONTRIBUTING.md says where each kind of change belongs, docs/architecture.md how the pieces fit, and docs/decisions.md why. SECURITY.md covers reporting and the threat model, PRIVACY.md what is stored and read.

lab/ replays attacks and everyday use against real Claude Code sessions, with and without AgentDetox (lab/README.md); its latest results are in lab/results/latest.md. The local hook performance suite is python -m bench.hook_latency --samples 100; recorded budgets and results are in bench/HOOK_LATENCY.md. python bench/accuracy_eval.py checks offline prevention, post-write evidence and recovery regressions without model calls. Its results and known misses are separate from the real-agent lab and are not a real-world accuracy estimate.

How a hook call flows: adapters.py turns an agent's event into a planned write or a shell command, engine.py runs the checks and reports signals, policy.py decides from your settings and the agent's abilities whether to block, ask or record, and the adapter formats the reply. hooks.py wires these together, and session.py runs the session-start check. The engine knows nothing about agents, so a new integration needs only an adapter. The detectors are in hidden.py and persistence.py (rules), provenance.py (copied text) and consistency.py (contradictions). Recovery objects are managed by integrity.py, transactional metadata by storage.py, the ledger by ledger.py, review actions by review.py, and the model server in daemon.py.

Installed hooks call a fixed executable, so updating it takes effect on the next hook call with no reinstall; a model server still running the old build is stopped by update.sh, and otherwise replaces itself on its next job. Re-run agentdetox install claude-code --apply only when agentdetox doctor says the registered hooks are from an older version. To remove everything: /plugin uninstall agentdetox or agentdetox uninstall claude-code, agentdetox daemon stop, then uv tool uninstall agentdetox, then delete ~/.agentdetox (this also deletes quarantined files).

The Claude Code plugin lives in plugins/agentdetox and the marketplace entry in .claude-plugin/marketplace.json; claude plugin validate . checks both. Its version, the version its hook script pins, and the package version must match (tests/test_plugin.py).

License

Apache-2.0