fix(config): reject malformed YAML before saving configuration

[rudycelekli]

Problem

Reject falsy non-mapping YAML and non-string keys before they can be treated as writable configuration. Empty and null documents remain supported.

Changes

• Reject list, boolean, numeric and string documents instead of silently replacing them on the next save.
• Reject non-string mapping keys before downstream key normalization can crash.

Verification

• Reproduced against unchanged main: focused regression tests 7 failed, 4 passed.
• Fixed branch: focused tests 11 passed; full suite 618 passed in 20.81s.
• Ruff check and git diff --check pass.
• MyPy still reports the same three pre-existing MCP SDK incompatibility errors as unchanged main; this patch adds none.

AI-assisted implementation and tests, independently reviewed before submission.

Formatting baseline: unchanged main already fails ruff format --check in 54 files; this PR does not reformat unrelated code.