Fix all 123 mypy type errors across 28 source files

[scottscott]

Summary

Resolves all 123 mypy strict-mode type errors present in the codebase. Where possible, fixes use proper type narrowing (isinstance, typing.List, explicit annotations) rather than # type: ignore suppressions. All 4,912 tests pass with these changes.

Key Changes

Structural improvements (checked by mypy, no suppressions):

• runtime.py — Use isinstance narrowing for 5 GovernanceDimension subclasses (ScopeCompliance, IsolationIntegrity, TemporalCompliance, HumanOverride, EthicalAlignment) instead of # type: ignore[attr-defined], so mypy verifies the subclass methods actually exist
• runtime.py — Declare _cert_store: CertificateStore | None = None in __init__ to replace hasattr guards with proper None checks
• store.py, authority.py, registry.py — Use typing.List in return annotations where a list() method on the class shadows the builtin, preserving downstream type visibility
• evaluator.py — Bundle JSON schemas inside the package (src/nomotic/schemas/) so importlib.resources can load them without fragile Traversable.parent traversal that only works from source checkouts
• api.py — Correct return types on 4 handler methods that returned wrong-arity tuples on error paths; use isinstance for playground scope dimension access
• scorecard.py — Fix reference to nonexistent report.all_gaps attribute; use explicit concatenation of critical_gaps + high_gaps + medium_gaps + low_gaps
• behavioral_provenance.py, cross_dimensional.py, fleet.py, workflow_governor.py — Replace max(d, key=d.get) with lambda k: d[k] to satisfy mypy's SupportsLessThan requirement on sort keys

Annotation and variable fixes:

• api.py, fleet_sim.py — Annotate module-level dicts/lists (_DIMENSION_META, DEPARTMENTS, BEHAVIOR_PROFILES) that mypy inferred as dict[str, object]
• cli.py — Rename conflicting variables, add union type declarations, and fix ~20 errors from DryRunResult typed as dict[str, object]
• runtime.py — Add assert verdict is not None narrowing before 3 GovernanceVerdict assignments
• pyproject.toml — Add types-PyYAML to dev dependencies (resolves 8 import-untyped errors)

Bug fix:

• sdk.py — Fix conn.close() in refresh_certificate() that was closing the wrong connection variable (conn instead of conn2)

Implementation Details

• 19 # type: ignore comments remain in the codebase — all are legitimate suppressions for known mypy limitations (tuple-length narrowing via len(), dynamic attribute patching on server contexts, BaseHTTPRequestHandler.server override, Windows-only ctypes.windll, and untyped third-party imports)
• No behavioral changes beyond the sdk.py bug fix — all other fixes are type annotations, variable renames, and structural improvements
• The bundled schemas in src/nomotic/schemas/ are copies of the existing root-level schemas/ directory; the originals are preserved for external tooling

assisted-by: Claude

🤖 Generated with Claude Code

[codecov]

Codecov Report

❌ Patch coverage is 82.72727% with 19 lines in your changes missing coverage. Please review.

Files with missing lines	Patch %	Lines
src/nomotic/cli.py	52.77%	17 Missing ⚠️
src/nomotic/api.py	93.33%	1 Missing ⚠️
src/nomotic/sdk.py	80.00%	1 Missing ⚠️

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