ops: add runtime health checks to doctor.sh

[benvinegar]

Adds runtime health checks to bin/doctor.sh, aligned with what the heartbeat monitors at runtime.

New checks

Check	Pass	Warn	Fail
Slack bridge	Responding on :7890	Not responding	—
Disk usage	<80%	≥80%	≥90%
Stale sockets	None	Has stale .sock files	—
Worktrees	≤5	>5 (suggest cleanup)	—
Session logs	<500MB	≥500MB (suggest pruning)	—

These checks run after the existing dependency/security/agent checks, so doctor.sh now covers both setup correctness and runtime health.

[greptile-apps]

Greptile Summary

Adds five runtime health checks to bin/doctor.sh: Slack bridge connectivity, disk usage thresholds, stale session sockets, worktree accumulation, and session log size. These complement the existing setup/dependency checks and align with what the heartbeat extension monitors at runtime.

• Critical bug: Three of the five new checks use $AGENT_HOME (lines 260, 279, 294–295), which is never defined in the script. The rest of doctor.sh consistently uses $BAUDBOT_HOME (defined on line 18). Because the script runs with set -euo pipefail, the undefined variable will cause the script to abort with an "unbound variable" error before reaching the summary section. This needs to be fixed before merging.
• Minor: The "Orphaned worktrees" section counts all worktrees (not just orphans) but uses a misleadingly-named ORPHANS variable.

Confidence Score: 2/5

• This PR has a script-breaking bug that must be fixed before merging — 3 of the 5 new checks use an undefined variable.
• The use of $AGENT_HOME instead of $BAUDBOT_HOME will cause doctor.sh to crash with an unbound variable error under set -u whenever any of the stale sockets, worktrees, or session logs checks are reached. The Slack bridge and disk usage checks work correctly. The fix is straightforward (replace AGENT_HOME with BAUDBOT_HOME in 4 places), but the script is broken as-is.
• bin/doctor.sh — the undefined $AGENT_HOME variable on lines 260, 279, 294, and 295 will crash the script

Important Files Changed

Filename	Overview
bin/doctor.sh	Adds 5 runtime health checks (Slack bridge, disk usage, stale sockets, worktrees, session logs). Contains a critical bug: uses undefined $AGENT_HOME instead of $BAUDBOT_HOME in 3 of the 5 new checks, which will crash the script under set -u.

Flowchart

%%{init: {'theme': 'neutral'}}%%
flowchart TD
    A[doctor.sh starts] --> B[User / Deps / Secrets / Runtime / Security / Agent checks]
    B --> C[Runtime Health section]
    C --> D{Slack bridge check}
    D -->|curl :7890 returns 400| D1[PASS]
    D -->|no response| D2[WARN]
    D1 --> E{Disk usage check}
    D2 --> E
    E -->|< 80%| E1[PASS]
    E -->|>= 80%| E2[WARN]
    E -->|>= 90%| E3[FAIL]
    E1 --> F{Stale sockets check}
    E2 --> F
    E3 --> F
    F -->|"⚠ Uses $AGENT_HOME (undefined)"| F0[CRASH: unbound variable]
    F -->|"After fix: uses $BAUDBOT_HOME"| F1{fuser finds stale .sock?}
    F1 -->|none stale| F2[PASS]
    F1 -->|stale found| F3[WARN]
    F2 --> G{Worktree count}
    F3 --> G
    G -->|<= 5| G1[PASS]
    G -->|> 5| G2[WARN]
    G1 --> H{Session log size}
    G2 --> H
    H -->|< 500MB| H1[PASS]
    H -->|>= 500MB| H2[WARN]
    H1 --> I[Summary]
    H2 --> I

Loading

_{Last reviewed commit: 946a9d2}

[greptile-apps]

_{1 file reviewed, 4 comments}

_{Edit Code Review Agent Settings | Greptile}

[greptile-apps]

Same $AGENT_HOME → $BAUDBOT_HOME fix needed

Suggested change

	WORKTREE_DIR="$AGENT_HOME/workspace/worktrees"
	WORKTREE_DIR="$BAUDBOT_HOME/workspace/worktrees"

Prompt To Fix With AI

This is a comment left during a code review.
Path: bin/doctor.sh
Line: 279

Comment:
**Same `$AGENT_HOME` → `$BAUDBOT_HOME` fix needed**

```suggestion
WORKTREE_DIR="$BAUDBOT_HOME/workspace/worktrees"
```

How can I resolve this? If you propose a fix, please make it concise.

[benvinegar]

Fixed (and that whole worktree-count block was later removed to keep the PR focused).

[sentry]

Bug: The disk usage check uses df / which can fail on systems with long filesystem names (e.g., LVM), causing the doctor.sh script to crash.
_{Severity: MEDIUM}

Suggested Fix

Modify the command to use the POSIX-compliant output format for df by adding the -P flag. This prevents line wrapping and ensures consistent output. The command should be df -P /.

Prompt for AI Agent

Review the code at the location below. A potential bug has been identified by an AI
agent.
Verify if this is a real issue. If it is, propose a fix; if not, explain why it's not
valid.

Location: bin/doctor.sh#L248

Potential issue: The `doctor.sh` script parses disk usage with `df / | tail -1 | awk
'{print $5}'`. On systems with long filesystem names, such as those using LVM or network
mounts, the output of `df` wraps to a new line. This causes the parsing logic to
incorrectly assign the mount point (e.g., `/`) to the `DISK_PCT` variable. Because the
script runs with `set -e`, the subsequent attempt to perform a numeric comparison `[
"$DISK_PCT" -ge 90 ]` on a non-numeric value will cause the script to exit with an
error, preventing the health check from completing.