Doer setup: add .doer.toml to finish onboarding

[doerapp]

Doer scanned this repo and produced a proposed .doer.toml, but the installation doesn't grant write access, so it can't open a PR. To finish setup, create .doer.toml at the repo root with the contents below and push to the default branch:

# .doer.toml — auto-generated by `doer init`.
# Generated: 2026-07-06T16:14:55Z
#
# Edit freely — Doer reads this file at the start of every run. The
# entries below scope which trees Doer will index (symbols, summaries,
# AGENTS.md). Anything outside these roots is ignored.
#
# Sources Doer used to infer this config:
#   - py_source_roots: fallback (top-level dirs with .py) -> ['engine', 'explainer', 'knowledge', 'scripts', 'tests']

[doer]
monitored_roots = ["engine", "explainer", "knowledge", "scripts", "tests"]
py_source_roots = ["engine", "explainer", "knowledge", "scripts", "tests"]
ts_source_roots = []

Every push after that will trigger Doer to refresh its index. (Granting the Doer app Contents: Read and write lets it open this as a ready-to-merge PR next time.)