Convex penalties for the alignment patching

[AndreaGuarracino]

This PR introduces:

• convex penalties for the patching
• mismatch/gap penalties tuning
• true extension alignment for heat/tail patching
• trigger patching a bit more often
• close indel detection during patching (to fix a bit bigger errors). This is triggered not too often as it can be very helpful, but expensive
• The 1st round of patching is aggressive, and the 2nd round is soft.

We pay in runtime and gain in alignment quality.