[ENHANCEMENT] Merge template into a single directory

[mtfishman]

Currently, the template is split into multiple directories in templates so parts can be selected when generating or updating packages, which is the design of PkgSkeleton.generate which we are calling out to. Instead, I think it would be better to merge them into a single template, and allow specifying a list of folders or files of that template to include or ignore when generating or updating packages.

An issue is that it may require invasive changes to PkgSkeleton.generate or rewriting a lot of that package here, which isn't ideal. However, we could still use PkgSkeleton.generate by creating temporary directories out of the selected folders and files so it still matches the folder structure expected by PkgSkeleton.generate.

[lkdvos]

An alternative option might be to have a single template, with some syntax to enable/disable certain parts of files, similar to how {PACKAGENAME} gets replaced with the correct package name. As a tentative example:

some part of the readme 
...
```{IF EXAMPLES}
## Examples

examples go here
```

[mtfishman]

That's an interesting idea, that is similar to JuliaFormatter's syntax for disabling formatting of certain codeblocks: https://domluna.github.io/JuliaFormatter.jl/stable/#Turn-off/on-formatting.

I think probably we want both, since we want better control over which folders and files get included or ignored, and additionally we want fine-grained control over whether or not certain parts of files get included or ignored.