[Patterns] Simplify pattern file structure

[compaluca]

Follow up on issue testable-eu/sast-testability-patterns#15.

Folder names and files in for pattern instances do not need to keep the pattern name. For instance, rather than 102_collection_taint_propagation/2_instance_102_collection_taint_propagation we could use 102_collection_taint_propagation/002

In addition consider using padding for filename. While it is possible to use ls -v, consider pading all numbers, i.e., 6 to 006, etc.