best-practices/agent-repos.md

Agent Repos & Container Agent Operations

Best practices for running AI agents via the agent-runtimes control plane — submitting tasks, using agent repos for persistence, running multi-model workflows, and monitoring progress.

Architecture Overview

The agent-runtimes system runs AI coding agents inside ephemeral Docker/K8s containers, orchestrated by a control plane (CP). The three-tier model:

1. Control Plane — central task queue, dispatcher registry, model routing. External systems (including Claude Code sessions) submit tasks here.
2. Dispatchers — poll the CP for tasks, resolve harness+model, create containers. All connections outbound (works behind firewalls).
3. Agent Containers — ephemeral, isolated. Receive a JSON payload, execute work, exit.

You (Claude Code session) → POST /tasks → Control Plane → Dispatcher → Agent Container
                           ← GET /tasks/{id} ← (poll for results)

Access

Environment	CP URL
K8s (port-forward)	kubectl port-forward -n agent-runtimes svc/controlplane 8100:8100 then http://localhost:8100
K8s (MFA)	https://agents.oreillyit.nz (behind Authelia)
Local dev (Docker Compose)	http://localhost:8100 after docker compose up -d

---

Submitting Tasks

Minimal Task

curl -s -X POST http://localhost:8100/tasks \
  -H "Content-Type: application/json" \
  -d '{
    "name": "Fix test_auth.py",
    "project_id": "my-project",
    "prompt": "Fix the failing test in test_auth.py",
    "harness": "planning-opus-repo/v1",
    "runtime": {"cli": "claude"},
    "pre_actions": [
      {"type": "clone", "repo": "git@gitea.oreillyit.nz-ai-enablement:skynet/my-project.git", "depth": 1}
    ]
  }'

Full Task Payload

{
  "task_id": "optional-uuid",
  "name": "Short name (shown in monitor)",
  "project_id": "groups tasks in monitor",
  "prompt": "The instruction for the agent",
  "harness": "composite-harness-name/v1",
  "runtime": {
    "cli": "claude",
    "model": "sonnet",
    "timeout": 1800
  },
  "priority": 0,
  "metadata": {
    "workflow": "my-workflow",
    "phase": "plan",
    "model": "opus"
  },
  "pre_actions": [
    {"type": "clone", "repo": "git@...", "branch": "main", "depth": 1}
  ],
  "on_success": [
    {"type": "commit_pr", "branch": "feature-branch", "title": "PR title", "base": "main"}
  ],
  "on_error": [
    {"type": "report", "webhook_url": "https://..."}
  ],
  "max_retries": 1
}

Key Fields

Field	Required	Description
name	Recommended	Short task name shown in the monitor
project_id	Recommended	Groups tasks in the monitor; enables filtering
prompt	Yes	The instruction sent to the agent
harness	Recommended	Composite harness (defines credentials, context, model provider)
runtime.cli	No	CLI runner: claude (default), openai_compat, agentic
pre_actions	No	Setup actions before agent runs (e.g., clone)
on_success	No	Post-agent actions on success (e.g., commit_pr, report)
on_error	No	Post-agent actions on failure
metadata	No	Arbitrary JSONB — used for workflow tracking, filtering
priority	No	-100 to 100 (higher = picked first, default 0)

Python Task Submission

For programmatic use from a Claude Code session:

import requests, json, uuid

CP = "http://localhost:8100"
task_id = str(uuid.uuid4())

payload = {
    "task_id": task_id,
    "name": "My agent task",
    "project_id": "my-project",
    "prompt": "...",
    "harness": "planning-opus-repo/v1",
    "runtime": {"cli": "claude"},
    "pre_actions": [{"type": "clone", "repo": "git@gitea.oreillyit.nz-ai-enablement:skynet/my-project.git"}],
    "metadata": {"workflow": "my-workflow", "phase": "plan"}
}

resp = requests.post(f"{CP}/tasks", json=payload, timeout=10)
data = resp.json()
print(f"Submitted: {data['task_id']}")

---

Available Harnesses

Harnesses define what credentials, context, and model provider an agent gets. Composites combine multiple layers.

Composite Harnesses (ready to use)

Harness	Model Provider	Capabilities
planning-opus-repo/v1	Anthropic Claude (subscription)	Planning context + SSH clone
planning-minimax-repo/v1	MiniMax	Planning context + SSH clone
python-code-review/v1	Default (Anthropic)	Python dev tools + Gitea admin

Context Layers (building blocks)

Layer	What it provides
planning/v1	Best-practices files for spec/plan writing
gitea-ssh/v1	SSH key for clone/push to Gitea
gitea-admin/v1	Gitea admin context (SSH + API token)
anthropic-cloud/v1	Anthropic API (subscription pricing)
minimax/v1	MiniMax API (SOPS-encrypted credentials)
code-methodology/v1	Coding methodology CLAUDE.md

Capability Layers

Layer	What it provides
python-dev/v1	pytest, ruff, mypy, hypothesis, uv

---

Monitoring Tasks

agent-monitor (terminal UI)

# Live view, filtered to your project
~/dev/claude/projects/agent-runtimes/scripts/agent-monitor --filter "project=my-project" --filter "age<20m"

# Single snapshot
~/dev/claude/projects/agent-runtimes/scripts/agent-monitor --once

# All running tasks
~/dev/claude/projects/agent-runtimes/scripts/agent-monitor --filter "state=running"

API Queries

CP=http://localhost:8100

# Check task status
curl -s "$CP/tasks/{task_id}" | python3 -m json.tool

# List tasks (most recent)
curl -s "$CP/tasks?limit=10" | python3 -m json.tool

# Cancel a task
curl -s -X DELETE "$CP/tasks/{task_id}"

Extracting Agent Output from Logs

Agents write to /workspace/.agent-output/output.md. To extract this from stream-json logs:

import requests, json

def extract_output(cp_url, task_id):
    """Extract output.md content from completed task logs."""
    r = requests.get(f"{cp_url}/tasks/{task_id}", timeout=10).json()
    logs = r.get("logs", "") or ""
    output = None
    for line in logs.split("\n"):
        if not line.startswith("{"):
            continue
        try:
            event = json.loads(line)
        except:
            continue
        if event.get("type") == "assistant":
            for block in event.get("message", {}).get("content", []):
                if isinstance(block, dict) and block.get("type") == "tool_use":
                    if block.get("name") == "Write" and "output.md" in str(block.get("input", {}).get("file_path", "")):
                        output = block["input"]["content"]
    return output

---

Workflows (Multi-Model Spec Planning)

Workflow templates define multi-step DAGs where different models collaborate, cross-review, and a human resolves disputes.

spec-planning v3

The flagship workflow for spec development. 14-node DAG:

Phase 0:   interview_a + interview_b (parallel, different models)
Phase 0.5: consolidate_questions
           ↓ HUMAN GATE — answer questions ↓
Phase 1:   plan_a + plan_b (parallel, different models)
Phase 2:   6 cross-reviews (spec/security/TDD × 2 models, each reviews OTHER's plan)
Phase 3:   escalate (surfaces disagreements, recommends best model)
           ↓ HUMAN GATE — resolve disputes ↓
Phase 4:   synthesize (best model writes final spec)

Running a Workflow Manually

Since the CP doesn't yet expand workflows natively, run each phase from a Claude Code session:

1. Render prompts — substitute {{ task_description }}, {{ scope_notes }}, etc. from the template YAML
2. Submit tasks — POST to CP with rendered prompts, correct harness per model
3. Wait — poll with agent-monitor or curl
4. Extract artifacts — read output.md from completed task logs
5. Inject artifacts — replace <<ARTIFACT:node_id:key>> sentinels in next phase's prompts
6. Human gates — present escalation output to user, collect answers, append to artifacts
7. Repeat for each phase

Artifact Passing Between Stages

When a downstream task needs an upstream task's output:

# Extract upstream output
upstream_output = extract_output(CP, upstream_task_id)

# Build downstream prompt with artifact injected
downstream_prompt = f"""
## Plan A (from upstream)
{upstream_output}

## Your Task
Review the above plan for security issues...
"""

Workflow Templates Location

Templates live in ~/dev/claude/projects/agent-runtimes/workflows/:

Template	Description
spec-planning.yaml	Full 14-node spec planning with cross-model review
comparative-plan.yaml	Simpler 5-node comparative planning

---

Agent Repos — Git-Based Persistence

What Is an Agent Repo

An agent repo is a Gitea fork of a project's main repo, named {repo}-agents (e.g., agent-runtimes-agents). Agents work on task-specific branches in the fork. All agent output is auto-committed to git before the container exits, so nothing is lost when ephemeral containers are removed.

Creating an Agent Repo

One-time setup per project. The fork must exist before agents can use it.

# Authenticate with the ai_admin token (see ~/dev/claude/secrets/gitea/ai_admin)
TOKEN="<token from secrets>"

# Check if fork exists (HTTP 200 = yes, 404 = no)
curl -sk -H "Authorization: token $TOKEN" \
  "https://gitea.oreillyit.nz/api/v1/repos/{org}/{repo}-agents"

# Create the fork (HTTP 202 = accepted, HTTP 409 = already exists)
curl -sk -X POST \
  -H "Authorization: token $TOKEN" \
  -H "Content-Type: application/json" \
  -d '{"organization":"{org}","name":"{repo}-agents"}' \
  "https://gitea.oreillyit.nz/api/v1/repos/{org}/{repo}/forks"

Naming Convention

Main repo	Agent repo
skynet/agent-runtimes	skynet/agent-runtimes-agents
skynet/brainiac-app	skynet/brainiac-app-agents

Always use the -agents suffix. The fork relationship enables cross-fork PRs.

Workspace Layout

/workspace/
├── reference/              # Owned by root — read-only (agent gets error if they try to write)
│   ├── main/               # Main repo default branch
│   ├── plan-opus-4f3a/     # Another agent's output branch (if needed)
│   └── best-practices/     # Best practices repo (if cloned)
└── working/                # Agent's branch of the agent repo (read-write)
    ├── CLAUDE.md           # Project code from the fork
    ├── spec/
    └── results/            # Starts empty — guaranteed output location
        ├── output.md
        ├── session-log.md
        └── changelog.md

• /workspace/reference/ — each subdirectory is a separate clone. Owned by root so agents get immediate permission errors if they try to modify.
• /workspace/working/ — the agent's branch. All changes auto-committed on exit.
• /workspace/working/results/ — always starts empty. Write outputs here.

Branch Naming

• With workflow context: {workflow_id}-{stage}-{short_task_id} (e.g., f58-plan-4f3a1b2c)
• Without workflow context: task-{short_task_id} (e.g., task-4f3a1b2c)

Auto-Commit (Finalize Phase)

After the agent exits (success or failure), the entrypoint runs finalize scripts:

1. Check for changes in /workspace/working/
2. git add -A && git commit with message: "Agent task {id} ({status}): {prompt_summary}"
3. git push origin {branch}
4. Write metadata to /workspace/.agent-output/ci_metadata.json

Finalize runs unconditionally — partial work from failed agents is preserved. Finalize failure does not override the agent's exit code.

Metadata Propagation

After container exit, the dispatcher reads ci_metadata.json and reports to CP:

{
  "agent_branch": "task-4f3a1b2c",
  "agent_sha": "a1b2c3d4...",
  "agent_repo_url": "git@gitea.oreillyit.nz:skynet/agent-runtimes-agents.git",
  "agent_branch_pushed": true
}

Stored in CPTask.metadata (JSONB dict). Query via GET /tasks/{id}.

Credential Separation

Actor	Credential	Purpose
Dispatcher	GITEA_API_TOKEN (read-only)	Verify fork and branches exist
Agent container	SSH key (via gitea-ssh harness)	Clone repos, push branches

The dispatcher verifies prerequisites but doesn't create forks or branches.

Retry Behaviour

On retry, the agent gets a fresh workspace (clean checkout from base branch). The previous attempt's branch is cloned into /workspace/reference/previous-attempt/ with a note in CLAUDE.md that the last attempt was incomplete and any work it created can be found there.

Cross-Repo PRs

When an agent working in the agent repo needs to create a PR against the main repo, Gitea supports cross-fork PRs natively. This is not automated initially — escalate to a human or handle on demand.

Branch Cleanup

Out of scope for initial implementation. The task- prefix and deterministic naming make automated pruning straightforward when needed.

---

Known Agent Repos

Project	Agent Repo	Created
skynet/agent-runtimes	skynet/agent-runtimes-agents	2026-04-05

---

Quick Reference

# Port-forward to CP
kubectl port-forward -n agent-runtimes svc/controlplane 8100:8100 &

# Submit a task
curl -s -X POST http://localhost:8100/tasks -H "Content-Type: application/json" \
  -d '{"name":"my-task","project_id":"my-project","prompt":"...","harness":"planning-opus-repo/v1","runtime":{"cli":"claude"},"pre_actions":[{"type":"clone","repo":"git@gitea.oreillyit.nz-ai-enablement:skynet/my-project.git"}]}'

# Monitor
~/dev/claude/projects/agent-runtimes/scripts/agent-monitor --filter "project=my-project" --filter "age<20m"

# Check result
curl -s http://localhost:8100/tasks/{id} | python3 -m json.tool

# Cancel
curl -s -X DELETE http://localhost:8100/tasks/{id}

---

Artifact Passing via Git Branches Instead of Env Vars

For multi-stage workflows where downstream tasks need upstream outputs, push artifacts to branches in an agent repo rather than embedding in prompts or env vars. This avoids K8s env var size limits (~228KB), survives pod restarts, provides a git audit trail, and scales to any artifact size. The downstream task clones the branch as a reference directory.

Protect Test Files from Agent Modification via Root-Owned Read-Only Clone

When agents run tests, they may "fix" failing tests by weakening assertions rather than fixing the underlying code. Prevent this by cloning the test suite into /workspace/reference/tests/ as a root-owned directory (the agent gets a permission error if it tries to write). The agent's working directory gets a symlink or copy of the tests at startup, but the authoritative copy is immutable. This is the same pattern as /workspace/reference/main/ for source code — root ownership makes modification a hard error, not a policy.

Infrastructure Failures Dominate Agent Failure Modes

In measured agent runs, the majority of task failures are infrastructure failures, not agent reasoning failures: network timeouts, SSH key not loaded, missing package in the base image, environment variable not propagated. Before debugging agent behaviour, check whether the failure is environmental — a task that consistently fails at "git clone" is an infrastructure problem, not an agent problem.

Concrete ratio: in one measured 12-task batch, 6/12 tasks failed and all 6 were infrastructure-class (wrong harness, missing payload fields, stale images) — zero model failures. Task templates that validate payload structure and harness compatibility before dispatch eliminate the entire dominant failure mode.

Pre-dispatch validation checklist:

• SSH key reachable from the agent harness (test clone before dispatching)
• Required env vars present (model API keys, registry credentials)
• Harness image has all required tools (uv, ruff, pytest, etc.)
• Target repo and branch exist
• Network egress allows required domains
• Task templates — long-term remediation. Validate payload structure and harness compatibility at template-render time, not via ad-hoc per-dispatch checks.

Invest in pre-dispatch validation scripts that catch the top-N infrastructure failures before the first agent container starts.

Cross-Model Reviews Catch ~38% More Issues Than a Single Model

Running the same security or spec review with two different models (e.g., Opus + MiniMax) and comparing outputs catches ~38% more issues than either alone — in measured reviews, only 62% of findings overlap. Models converge on obvious issues but diverge on edge cases and design concerns. Worth the extra cost for security-critical specs and architecture reviews; overkill for routine code review.

Pattern: dispatch parallel review tasks to different models with identical prompts, union the findings, deduplicate against a shared issue key (file + line + category). Present the merged list to the human reviewer along with per-model attribution so reviewers can see where models agreed vs. diverged.

Agent Worktree Branches Contain Files, Not Commits — Copy, Don't Merge

Symptom: Orchestrator merges an agent's branch and sees "Already up to date" because the agent wrote files to its worktree but never ran git add / git commit. Downstream tasks that depend on the upstream artifact then fail or silently use stale data.

Fix: Orchestration must explicitly copy files from dependency worktrees (driven by a writes field in the task manifest) into the consuming worktree. Git merge is insufficient when agent output is untracked.

Alternative: Require agents to commit before exit (finalize phase auto-commits everything under /workspace/working/), which unlocks git-branch artifact passing. The finalize-phase auto-commit described above is the canonical implementation — enforce it for any agent whose output other tasks depend on.

Include Exact Dataclass/Context Schemas in Template-Writing Agent Prompts

Symptom: Agents writing templates invent their own mock context objects (e.g., dict-style model["fields"]) while real code provides a different shape (e.g., dataclass model.fields). Templates render against the mocks but produce attribute errors against real objects during integration.

Fix: Always include exact dataclass/type definitions of the render context in the agent prompt. During review, compare each agent's mock objects against the real normalized types before merging. Treat "wrote its own mock shape" as a review-blocking issue — the mock shape is a contract the agent must follow, not invent.

Never Assume Web Search in Container Agents; Validate Version-Specific Claims Separately

Symptom: Agents in Docker/K8s containers have no WebSearch or WebFetch capability even with --dangerously-skip-permissions. Version numbers, release dates, and "actively maintained" claims come from training data and are often wrong (~30% inaccuracy on package versions in measured runs).

Fix:

• Never tell a container agent to "use web search" — it has none and will silently fabricate from training data.
• Run a separate web-validation pass (Opus or similar with network access) after research agents complete.
• Treat all version claims as hypotheses until validated.
• Budget web validation as a distinct pipeline stage, not an afterthought.

Cost-Effective Models Need Explicit Scope Boundaries

Smaller/cheaper models (e.g., MiniMax, Haiku) need tighter scope constraints than capable flagship models. Without explicit boundaries, they drift into scope creep, run the full test suite when asked to write tests, or attempt broad refactors. For cost-effective model tasks:

• No full test suite runs — specify which test file or test ID to run
• Concrete patterns, not open-ended — "Write a test matching test_cp_*.py naming" not "Write tests for the control plane"
• Longer timeouts — cheaper models are often slower per token; set runtime.timeout to 2-3× what flagship models need
• Explicit output location — "Write to results/output.md" not "Write your findings"

Treat scope boundaries as a harness concern, not an agent concern — encode them in the prompt template or harness context, not in ad-hoc task prompts.