Convert call sites to use typed commands (part 1)

[robertbrignull]

This PR converts some places that call commands to use typed commands. This isn't everything but I'll try to open a few smaller PRs instead of one giant PR. That way it'll be easier to review and easier to adapt thoughts and ideas before getting too deep into things.

Each commit converts a single file, so if you want to review commit-by-commit then that is an option.

This PR involves:

• Documenting new builtin commands whenever we encounter a new one.
  • I'm working out parameter types from the usages we have in the codebase and from the VS Code docs.
• Passing either App or AppCommandManager to wherever it is needed.
  • When deciding between the two, my thought process so far has been that when we're constructing a long-lived class like VariantAnalaysisManager then give it the full App, but when it's a standalone function that triggers commands but doesn't do anything else then give it just the AppCommandManager.
  • I'm happy to do things differently if there's tangible benefit. It's also worth noting we can change arguments to functions easily, so none of these decisions will block progress in the future.

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.

[robertbrignull]

Ugh, lots of test compilation errors. Somehow I never spot these locally. 😞

[robertbrignull]

Test should all be fixed now. Things compile for me locally. I've rebased the changes into the original commits, so you can see which changes necessitated which other changes.

[koesie10]

Perhaps add a comment for this command? It's not entirely obvious if you're just looking at the file that this is a command added by VS Code on custom views.