[algorithm] Clean up of the InsertionAlgorithm class

[th-skam]

Main changes

1. Renamed DetectionOutput variables

Detection output variables have been renamed to better reflect their intended purpose:

• collisionOutput: needle-surface proximity pair during the puncture
• insertionOutput: needle-volume proximity pairs during the insertion phase

2. Renamed links to BaseGeometry objects.

Previous naming convention gives emphasis on the directionality of the detection. l_from and l_dest (or l_fromVol / l_destVol) imply how proximity pairs were computed (from -> destination geometries). The user shouldn't be concerned with this.

The InsertionAlgorithm is tailored for needle insertion. In the scene, the user must specify the BaseGeometry specializations that correspond to the nodes of the:

• Needle Tip: detects proximities during puncture AND insertion
• Needle Shaft: used to couple proximities detected within the volume
• Surface: of the object to be punctured
• Volume: of the object within which the needle is inserted

The new names reflect these roles and signify that the links are formed between the algorithm and BaseGeometry components.

3. Renamed Operations functions and proximity objects

Following the same logic, all the function pointers instantiated from the Operations namespace have been renamed to clearly indicate:

• The type of operation
• The geometry it is applied to
• The type of proximity returned (tip, shaft, surface, volume)

Minor changes

• Renamed threshold variables related to:
  • Puncture force (punctureThreshold)
  • The tip advancing inside the volume (tipDistThreshold)
• Removed commented-out variables and overused sofa:: namespace qualifiers
• Simplified verbose template syntax with typedef for re-used multi-argument types
• Renamed variables for the draw function, made points transparent and drawing is disabled by default
• Grouped variable definitions by type and functionality
• Simplified pointer validity checks
• Code formatting using .clang-format shipped with main SOFA