Fix assumption on unchanging MRCA node index

[kche309]

• FLC assumes the node number of the MRCA of a clade does not change during MCMC (this is only true when there is very high certainty on the topology of the tree).
• To modify code so the MRCA clade number used by FLC is updated during MCMC
• Test changes using integration test/unit test with topology changing operator (e.g., subtree slide) that changes the MRCA node of a clade