gemini-batch-execution

name	gemini-batch-execution
description	Execute Gemini research tasks in efficient batches using hermes router to maximize $20/month quota utilization. Covers toolset config, batch patterns, sandbox pitfalls, and cleanup.
version	1.0.0
category	ai
type	skill
trigger	manual
auto_execute	false

Gemini Batch Execution

Execute Gemini research tasks in efficient batches to maximize the $20/month subscription. Two execution modes exist — pick based on task type.

When to Use

• Research/standards mapping tasks
• Literature gathering and textbook acquisition
• Competitive intelligence or market scanning
• Any read-heavy, write-output task that benefits from Gemini's 1M context and web access

MODE 1: Direct Local Execution (PREFERRED for repo work)

For tasks that touch the local filesystem (cataloging, indexing, running scripts, closing GitHub issues), use execute_code + delegate_task subagents instead of h-router-gemini. This is 5-10x faster with NO sandbox isolation issues.

Why: Lessons from Overnight Batch (33 issues in one session)

• delegate_task with up to 3 parallel subagents runs independent filesystem work concurrently
• Subagents have direct repo access — no git commit failures, no -2 duplicate files, no sandbox state conflicts
• gh issue close + gh issue comment for cleanup without shell alias escaping issues
• One Hermes CLI session can close 30+ issues by doing lightweight filesystem ops directly

Pattern: Filesystem Triage + Parallel Subagents

# Step 1: List all gemini-assigned open issues
gh issue list --label "agent:gemini" --state open --json number,title,labels

# Step 2: Categorize by priority and batch (HIGH/MED/LOW)

# Step 3: For independent filesystem tasks, dispatch parallel subagents
delegate_task(tasks=[
    {"goal": "Scan and catalog <source_dir>...", "toolsets": ["terminal", "file"]},
    {"goal": "Triage /path/to/archive/...", "toolsets": ["terminal", "file"]},
    {"goal": "Catalog /path/to/refs/...", "toolsets": ["terminal", "file"]},
])

# Step 4: For tasks executable via existing scripts, run directly
uv run python scripts/document-intelligence/batch-process-standards.py --domain materials

# Step 5: Close issues with results
gh issue close <num> -c "Result summary here."
gh issue comment <num> -b "Detailed findings..."

What NOT to do in local mode:

• Don't run LLM web research — delegate_task subagents can't do web_search
• Don't run tasks needing Gemini's 1M context window — subagents inherit your model, not Gemini
• Don't parallelize tasks that touch the same files — use separate subagents for separate dirs

When to use Mode 1 vs Mode 2:

Task Type	Mode
Filesystem scan/catalog	Mode 1 (direct)
Run existing scripts	Mode 1 (direct)
Close/update GitHub issues	Mode 1 (direct)
Web research, standards lookup	Mode 2 (h-router-gemini)
Large doc ingestion (1M context)	Mode 2 (h-router-gemini)
Literature gathering with ISBNs	Mode 2 (h-router-gemini)

MODE 2: h-router-gemini CLI (for web research)

Execute tasks via the Hermes router for tasks needing web access or Gemini's 1M context. Each session costs ~1-2 queries of the monthly quota — minimize sessions, maximize tasks per session.

Working Command

h-router-gemini -t terminal,file,web -q "$(cat /tmp/gemini-task-prompt.txt)"

Do NOT use h-gemini — its --base-url flag syntax is broken in current Hermes versions. h-router-gemini (openrouter provider) works correctly.

Toolset

Always use -t terminal,file,web:

• file: read_file, write_file, search_files — needed for codebase scanning and file creation
• terminal: run commands (git add, git commit, find, head) — needed to persist output
• web: web_search, web_extract — needed for live research

CRITICAL: web_search is unreliable. In multiple sessions, Gemini reported "I do not have a web_search tool" despite -t web. When this happens, Gemini falls back to internal knowledge. For research-heavy tasks, this means:

• Task output will include "Limitation Note: Live web searches could not be performed"
• Content may be stale or incomplete
• Strategy docs and plans are still useful; factual data (ISBNs, prices, URLs) may be placeholder

Workaround: If web_search fails, explicitly instruct Gemini in the prompt to "use known knowledge and document limitations" — otherwise it may loop trying to find the tool.

Batch Pattern

Write ALL tasks into ONE prompt file. Gemini can handle 5-6 distinct tasks in a single session (each producing a file + commit).

/tmp/gemini-batch.txt:
  ┌─────────────────────────────┐
  │ TASK 1: Standards Gap ...   │
  │ TASK 2: SubseaIQ Data ...   │
  │ TASK 3: Textbooks Plan ...  │
  │ TASK 4: Speech-to-Text ...  │
  │ TASK 5: OSS Tools Update..  │
  │ TASK 6: Marine Hydro Ref..  │
  │                              │
  │ RULES:                       │
  │ - Order: 1,2,3,4,5,6        │
  │ - Commit after each         │
  │ - Do NOT git push           │
  │ - Overwrite files in place  │
  │ - No -2 versions            │
  └─────────────────────────────┘

Per-Task Template

Each task in the batch follows this pattern:

══════════════════════════════════════════
TASK N: Name and Description (#issue)
══════════════════════════════════════════

1. Read/scan existing codebase or data (use search_files, read_file, terminal find/grep)
2. Research via web_search if needed
3. Create file at: docs/document-intelligence/standards-mapping/filename.md or notes/prep/filename.md
4. Commit: git add <file> && git commit -m "descriptive message (#issue)"

Do NOT push to remote after commits.

Critical Pitfalls

1. Sandbox isolation: Gemini executes in an isolated sandbox. Files it creates can be destroyed when the session ends. The ONLY way to persist is for Gemini to successfully run git commit before the session terminates. Always verify with git status --short and git log after the session.

2. Session timeout: Sessions can timeout or abort mid-task. Always instruct Gemini to "commit after each task" so partial work is saved. If a session completes 3 of 6 tasks, the first 3 are already committed.

3. No -2 versions: Gemini sometimes creates duplicate files (file-2.md) when it cannot write to the original path (sandbox state conflict). If you see -2 versions, move the content to the original and remove the duplicate before committing.

4. Git commit failures in sandbox: Even after writing files successfully, Gemini's git commit can fail with exit 1 due to sandbox isolation. Always have a fallback plan: if Gemini's commits fail, check the files on disk, and commit them manually via terminal/homes session.

5. Empty-content crash (FATAL): Gemini can hit "Max retries for empty content" errors (think blocks with no actual response) and die completely. When this happens:

   • The session exits immediately, abandoning ALL remaining tasks
   • Files written before the crash ARE committed (if commit succeeded before crash)
   • Remaining tasks are silently skipped — NO error message in the script output beyond the crash log
   • Detection: After batch runs, check tail -100 <logfile> for "Max retries (3) for empty content exceeded" and verify all issues are closed. Manually complete the remaining tasks immediately — don't retry Gemini.

6. Alias resolution in scripts: h-router-gemini is a shell alias and WON'T expand in non-interactive bash scripts. Always wrap it as a shell function before calling in scripts:

   h-router-gemini() { hermes chat --provider openrouter -m google/gemini-2.5-pro "$@"; }
   

7. Sequential only: Multiple Gemini sessions can't commit simultaneously. Run sessions sequentially, not in parallel.

Nightly Cron Automation (IMPLEMENTED — #1961)

A nightly cron job auto-processes agent:gemini issues. No manual batching needed for triage-level work.

Scripts

• scripts/cron/gemini-nightly-batch.py — Python processor (queries issues, classifies, processes/queues)
• scripts/cron/gemini-nightly-batch.sh — Bash wrapper (git-safe, workstation guard, state commit)
• Schedule: 0 23 * * * (23:00 UTC) — declared in config/scheduled-tasks/schedule-tasks.yaml

How the classifier works

• Labels containing cat:research, cat:document-intelligence, dark-intelligence, domain:marine, domain:standards → Mode 2 (router)
• Everything else → Mode 1 (local triage)
• Self-referencing meta issues (like #1961 itself) are auto-excluded
• Issues sorted by priority label (high → medium → low)
• Capped at 10 issues per run (safety)

Reports

• JSON batch reports written to .Codex/state/gemini-batch/batch-YYYY-MM-DD.json
• Reports are gitignored (ephemeral state), but auto-committed by the bash wrapper if not ignored

Stale tracking issues

When reviewing pending Gemini work, always check if referenced sub-issues are already CLOSED before processing. The #1976 tracking issue listed 4 pending tasks — all were already done. Check with:

for i in <issue_numbers>; do gh issue view $i --json state --jq '.state'; done

Manual Overnight Batch Execution via Hermes Cron

For tasks that genuinely need Gemini's 1M context or web research (Mode 2), use Hermes cron jobs:

cronjob create \
  --name "gemini-overnight-batch-1" \
  --model "google/gemini-2.5-pro" \
  --provider "openrouter" \
  --schedule "0 1 * * *" \
  --deliver "origin" \
  --prompt "<self-contained prompt>"

CRITICAL: The cron prompt must be fully self-contained (no external file refs, no $(cat file)). All file paths must be absolute. The cron session has the same toolset but may not have OPENROUTER_API_KEY in env — if Gemini fails to route, fall back to running h-router-gemini via terminal command in the prompt.

Schedule batches 60-75 minutes apart to avoid rate limits and ensure each session completes before the next starts.

Post-Session Cleanup Checklist

cd /mnt/local-analysis/workspace-hub
# 1. Verify what Gemini committed
git log --oneline -5
git status --short

# 2. CRITICAL: Clean up duplicate commits from Gemini's retry loops
# Gemini often retries git commit and creates 2x commits for the same work
# Pattern: 5 commits followed by 5 identical commit messages
git reset --soft HEAD~N  # where N = number of duplicate commits
git reset HEAD -- .
git add <files>
git commit -m "clean single commit message (#issue)"

# 3. Check for duplicate files (-2 versions)
find . -name "*-2.*" 2>/dev/null
rm -f notes/prep/*-2.md docs/document-intelligence/*-2.md  # then keep originals

# 4. If Gemini created files but couldn't commit, commit them manually
git add <files>
git commit -m "feat(doc-intel): <description>"

# 5. Close completed issues
gh issue close <num> -c "<brief result summary>"

# 6. Update agent-work-queue.md
./scripts/refresh-agent-work-queue.sh

Critical Pitfall: uv run suppresses stdout in sandbox subprocesses

When running scripts via uv run python script.py, ALL stdout output from the script is swallowed by the sandbox layer. Print statements, progress messages — all disappear. This causes "silent failures" that appear to succeed.

Workarounds:

1. Write progress/results to a log file (NOT stdout) and read it back with read_file
2. Use process() with background=true and follow_output=true for long-running tasks
3. Write to a file at each step, then read_file to check progress
4. Use terminal("... > /tmp/log.log 2>&1; cat /tmp/log.log") to force output via cat

DO NOT: rely on print() output from uv run scripts — it will vanish.

Expected Efficiency

• 5-6 research tasks per session
• ~5 minutes per session (600s timeout usually enough)
• ~25-30 tasks for the entire $20/month quota
• Each task produces: 1 file + 1 commit + 1 issue close
• Overnight: schedule 4 cron jobs 60-75 min apart = 20 issues per night