Initial commit: pygenium as git submodule

tasks/03-agent-runner.md

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+# 03. Sub-agent runner with createAgentSession
+
+meta:
+  id: pygienium-03
+  feature: pygienium
+  priority: P1
+  depends_on: [pygienium-01]
+  tags: [infrastructure, core]
+
+objective:
+
+- Build `src/agent-runner.ts`: spawn isolated child pi sessions via `createAgentSession`, capture transcripts/results, and return a typed result — the engine that powers every check's sub-agent phases.
+
+deliverables:
+
+- `src/agent-runner.ts` exporting `runAgent(options)`, `AgentRuntimeModel`, `RunAgentResult`, `AgentRunError`, `buildRuntimeHeader`, `RuntimeContext`
+- Each run writes `pygienium/runs/<runId>/{prompt.md, transcript.jsonl, result.md, error.txt}`
+- Inherits parent model + modelRegistry + thinkingLevel (so child phases reason at the same depth)
+- AbortSignal support; `onEvent` forwarding hook for UI streaming
+- Child tools: the built-in edit/write/read/bash surface; noExtensions: true (avoid recursion)
+
+steps:
+
+- Port piolium's `agent-runner.ts` shape: composed system prompt = runtime header + agent systemPrompt; `DefaultResourceLoader` with noExtensions/noThemes/noContextFiles; in-memory SessionManager
+- Define `AgentDefinition` interface (name, description, systemPrompt, allowedTools, sourcePath) consumed here
+- Wire `session.subscribe` to capture final assistant text + stopReason + errorMessage
+- Handle abort: add/remove abort listener, call `session.agent.abort()`
+
+tests:
+
+- Unit: `buildRuntimeHeader` includes cwd, mode, phase, assigned output paths
+- Integration: run a smoke agent (no-tools, replies with a fixed string) via `runAgent`; assert result.text non-empty and transcript.jsonl exists
+
+acceptance_criteria:
+
+- `runAgent` returns RunAgentResult with text + transcriptPath + durationMs
+- Aborting the signal cancels the child session without leaving it running
+- A child that errors throws `AgentRunError` carrying the result
+
+validation:
+
+- Invoke a smoke run from a temporary command and inspect the runs dir
+
+notes:
+
+- This is the most direct piolium port; keep it faithful to reduce risk
+- Do NOT load extensions in the child (footgun) — `noExtensions: true`