Allow Redundant Paths to Consider Indels

[evolvedmicrobe]

Before the redundant path purger could only remove SNPs, this allows it to call paths like A -> B -> F / A->C->D->E->F as redundant, simplifying the graph quite a bit.

Changes include:

• Make PathWithOrientation class to be internal to the assembly
• Remove redundant null check on pass graph
• Allow paths to converge if they have different lengths but wind up at same end node
• Verified that the paths not only end on the same node, but also approach it from the same direction

The checking for loops needs to be much faster than it is.