refactor: migrate all extension commands to the new project model

This MR changes the parameter of every command from the old, soon-to-be-replaced, WrappedRepository to the new `ProjectInRepository' type.

The old and the new model can't be used as a source of truth at the same time. The user sets them up differently, and there would be inconsistencies in more complex scenarios (multiple repositories, multiple git remotes). So we temporarily have to introduce a translation method that translates the old model to the new one. Eventually, we'll get the model from GitLabProjectRepository, but now we still get it the old way and then translate it to the new object structure.

Where do the commands get their parameter from now?

graph LR;
A[getActiveRepositoryOrSelectOne] -- "produces WrappedRepository" --> B[convertRepositoryToProject]
B -- "produces ProjectInRepository" --> C[extension command]

And this is how will the commands get it when the migration is complete

graph LR;
A[getActiveProjectOrSelectOne] -- "produces ProjectInRepository" --> B[extension command]

The implementation

1. The getActiveRepository moved from git_extension_wrapper to the run_with_valid_project module. This way the git_extension_wrapper can focus on basic interaction with VS Code Git extension and not on additional business logic.
2. The runWithValidProject method changed signature to the new model and uses the convertRepositoryToProject method to translate the old model to the new model
3. The commands are migrated in small chunks to the new model (in separate commits that still work and pass tests)

This MR might be best-reviewed commit-by-commit.

There is no change to user-facing behaviour.

Related to #558 (closed)