test_snap_versions lint failure due to snapshot key ordering mismatch (and stale snapshot persistence)

Description of the bug

Description
I have encountered two related behaviors regarding nf-test snapshots and nf-core modules lint that lead to false failures and stale data management issues.

Bug 1: Snapshot Ordering Mismatch causes Lint Failure
When a module has multiple tests (e.g., a script test and a stub test), the order in which entries appear in the *.nf.test.snap file can drift from the order in main.nf.test. This causes nf-core modules lint to report missing versions, even when they exist.

Steps to Reproduce:
Create a module with two tests in main.nf.test:

Test A: A "real" script test (initially configured without snapshotting output/versions).

Test B: A stub test (configured with assertions/snapshots).

Run nf-test test.

Result: main.nf.test.snap is created containing only Test B data.

Modify Test A to assert/snapshot versions.yml.

Run nf-test test again.

Result: Test A data is appended to the bottom of the existing main.nf.test.snap.

Current File State:

main.nf.test: Order is [Test A, Test B].

main.nf.test.snap: Order is [Test B, Test A].

Run nf-core modules lint.

Observed Behavior:
The linter fails with the error:

test_snap_versions: versions not found in snapshot
This occurs because the linter appears to expect the snapshot keys to appear in a specific order or struggles to parse the versions when the script test appears after the stub test in the snapshot file.

Expected Behavior:
The linter should be able to identify the versions block regardless of its position in the snapshot file relative to other tests, OR nf-test should respect the source file order when updating snapshots.

Bug 2: Stale Snapshot Persistence (Silent Passing)
Additionally, I observed potentially suboptimal behavior regarding outdated version files.

Observation:
If a snapshot previously contained a versions file check, and the test is subsequently modified to remove that check (or the file is no longer generated), the old entry remains in the *.snap file. nf-test passes successfully because it ignores the extra data in the snapshot, effectively skipping verification for that section.

Resolution:
I had to manually delete the .snap file and regenerate it to clear the stale version entries.

Command used and terminal output

System information

nf-core, version 3.5.1
nf-test 0.9.2

Reproduce the two cases using main.nf.test and main.nf.test.snap, then trace snapshot generation and the test_snap_versions lint check. Done means versions are found regardless of snapshot key order, and removed checks no longer leave stale snapshot data; add regression coverage for both behaviors.