Put the last 14 files under the type gate, and fix what they were hiding

[dovvnloading]

Problem

The gate said "339 source files" and meant it — but "all of them" was never
verified. Checking [tool.mypy].files against the tree found three directories
with Python in them that nothing was checking:

directory	files	state
plugins/	8	6 errors
mutation_tests/	5	clean
tests_e2e/	1	clean

What plugins/ was hiding

plugins/system_prompt/plugin.py, two kinds of error:

root = document.get_branch_root(parent_node_id)
... edge.target == root.id

get_branch_root returns SceneNode | None — None for an id it does not
know. It cannot be None here: the guard fifteen lines up already returns
early for a parent_node_id that is not in document.nodes. Rather than assert
that with an ignore, the None branch now returns _create_pending() — the
answer this plugin already has for "no usable parent", and the difference
between an AttributeError and a sensible fallback if that guard ever changes.

The other four were the familiar unnarrowed node state, in a generator that read
document.nodes[edge.source] three separate times. A checker cannot tie a kind
check on one subscript expression to a field read on another — and neither can a
reader. It is a plain loop over one bound candidate now, with the same result:
first match in edge order, or None.

Two settings come with plugins/

namespace_packages and explicit_package_bases. plugins/ is eight sibling
directories each holding a plugin.py with no __init__.py anywhere — the
layout the loader discovers by path — and without those two, mypy maps all eight
onto one module name and refuses to check any of them ("Duplicate module named
'plugin'"). Verified they change nothing for the existing files: the run is
clean before and after.

Result

• The gate covers 353 source files.
• The coverage check now reports no uncovered directory and no uncovered root
  module.
• Verified it still bites by injecting a deliberate type error into a plugin, a
  mutation test and api_provider — caught in all three.

Test plan

• Full suite: 3,285 passed, 20 skipped.
• The System Prompt plugin's own 23 tests pass.
• ruff check . clean. mypy clean across 353 files.

🤖 Generated with Claude Code