Restructure methods database to avoid redundant information in path

Take the httomolibgpu methods database info as an example, this is the directory structure of the dir `httomo/methods_database/packages/external/httomolibgpu/`:
```
[twi18192@pc0074 httomolibgpu (param-sweep-runner)]$ tree -L 1
.
├── httomolibgpu_modules.yaml
├── httomolibgpu.yaml
├── __init__.py
├── __pycache__
└── supporting_funcs
```

The directory is named `httomolibgpu/`, so it can be assumed that files in it all are relating to httomlibgpu. Therefore, I think that having files within it called:
- `httomolibgpu_modules.yaml`
- `httomolibgpu.yaml`

which contain the term `httomolibgpu` is redundant.

Another point to mention is that the file `httomolibgpu.yaml` has no indication whatsoever what information it contains, it's entirely dependent on the developer knowing what is in there (which is the information of all the methods in the httomolibgpu package, such as `pattern`).

I have a few suggestions:
- remove redundant package name from files within directories whose name are packages
- rename the `package.yaml` to something else that indicates that it contains methods info, maybe `methods.yaml`? (Ie, rename `httomolibgpu.yaml` to `methods.yaml`)

This would result in a directory structure like the following:
```
├── modules.yaml
├── methods.yaml
├── __init__.py
├── __pycache__
└── supporting_funcs
```

which I think is a bit easier to understand.

Other suggestions are welcome! :slightly_smiling_face: