[Patterns] Consistent import of paradigms / patterns

As noted in #92 (closed), it is not obvious that the same args must be passed to the CLI when we we build the patterns and when we do some subsequent operations. This often leads to unwanted side-effects: one forgets which parameters were passed to the paradigms, etc.

This MR:

• Uses the now central Metadata class to extract any relevant information to rebuild identically the paradigms
• Same to read the patterns
• Simplifies the code: one single md.get_paradigms() / md.get_patterns() method allows to read paradigms or patterns based on the previous run.

Benefits:

• Easier to maintain (see how it reduces the code!)
• Clearer for the user

TODOs:

• Restore cell sampling after pattern computation
• Document this behaviour

Closes #95 (closed)