Convert call sites to use typed commands (part 3)

[robertbrignull]

Follows on from earlier PRs and converts some more places to call typed commands.

The only non-trivial bit of this PR is around VariantAnalysisMonitor:

• This class already took credentials, but in this case I decided to instead provide a full app and moved it to the constructor instead of the monitorVariantAnalysis method.
• The tests were asserting that the codeQL.autoDownloadVariantAnalysisResult command was called, but then also asserting that the VariantAnalysisManager. autoDownloadVariantAnalysisResult method was called. This only works if it's actually executing commands rather than using a mock, and is also not very necessary. I decided to remove these and just check that the command was called, and this made the tests a lot simpler.

Checklist

• CHANGELOG.md has been updated to incorporate all user visible changes made by this pull request.
• Issues have been created for any UI or other user-facing changes made by this pull request.
• [Maintainers only] If this pull request makes user-facing changes that require documentation changes, open a corresponding docs pull request in the github/codeql repo and add the ready-for-doc-review label there.

[koesie10]

It feels strange to be passing in both the context and the app. I believe both of the properties that this class accesses on the context (extensionMode and extensionUri) also exist on the app as mode and extensionPath. I think it would be best to switch to those in this PR as well, even though the change is unrelated.

[robertbrignull]

That sounds good to me. I didn't really have it clear in my head what the point of ExtensionContext was and how it relates to the app, but I see now the app can replace the extension context in some places. The context is stored as a field on the app, so it can act as a platform-independent interface to those values.

I can take a look (not in this PR) to see if there are more places where we pass both types and if it could be simplified.