fix(runtime): preserve config when drop-ins are disabled

[efegokdemir]

Description

Fixes #2123. When --drop-in-config or RUNTIME_DROP_IN_CONFIG is empty, containerd and CRI-O now update the loaded configuration directly. Previously, both engines still created a drop-in-only destination while the CLI or installer wrote to the top-level config path, which could overwrite existing runtime settings or leave the NVIDIA runtime missing.

CRI-O cleanup continues to use its explicitly loaded top-level destination when removing the NVIDIA runtime. Regression tests cover CLI configuration for both engines, installer setup for both engines, and CRI-O cleanup with distinct source and destination configs.

Checklist

• No secrets, sensitive information, or unrelated changes
• Unit tests passing (make test)
• Lint checks passing (make lint) — the full-repository lint reports six existing SA4023 issues in cmd/nvidia-cdi-hook/update-ldcache/update-ldcache.go and internal/ldconfig/ldconfig.go; the same failures reproduce on pristine main. All changed packages pass targeted lint.
• Test cases are added for new code paths
• Commits are signed-off and cryptographically signed

Testing

• make build — passed
• make test — passed
• golangci-lint run on the five changed package paths — passed, 0 issues
• make lint — fails on the six unrelated SA4023 findings above; verified on pristine upstream a672e378
• make fmt and git diff --check — passed
• Fail-before evidence: the new CLI regression test failed on pristine a672e378 for both runtimes. CRI-O lost its existing crun default, while containerd wrote a self-referential import and omitted the NVIDIA runtime. The same tests pass with this change.

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