========== In TRUNK ==========

Ported feature TRANSFER

Log overview (see previous logs for more details)
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NEW
  * Added 2 parameters TRANSFER_INS_RATE and TRANSFER_REPL_RATE to set the rate of insertion (resp. replacement) transfer.
    Default: 0.0 => No transfer.
    Both rates are per replication rates and trigger a transfer attempt (the actual occurrence of a transfer event will depend on whether an alignment is found). There can be at most one transfer of each type per replication.
  * Every possible ae_mutation now has a _length
  * Added method ae_dna::copy_into_new_GU( int32_t pos_1, int32_t pos_2 ) const
  * Added method inline void ae_genetic_unit::copy_promoters_included_in( int32_t pos_1, int32_t pos_2, ae_list** new_promoter_lists )
  * An ae_vis_a_vis now contains its score
  * Added a header for R in the output file of fixed_mutations
  * Added a new post-treatment "mutagenesis"
  * Added checking options (NO_CHECK / LIGHT_CHECK / FULL_CHECK) to the "fixed_mutations" post-treatment
  * Added a log file for transfer. Keyword TRANSFER, file name log_transfer.out
  * Added a test case for transfer.
  * New file ae_enums.h
  
MODIFIED
  * Moved the replication procedure to ae_population.
  * Deported the genome size barrier checks one level up ( e.g. from do_deletion( pos_1, pos_2 ) to do_deletion() and do_rearrangements_with_align() ).
  * Method void ae_genetic_unit::copy_lagging_promoters_starting_between( int32_t pos_1, int32_t pos_2, ae_list* new_promoter_list ) no longer has the ( pos_1 > pos_2 ) prerequisite
  * Renamed class utils to ae_utils
  
BUGFIX
  * Replaying a translocation when alignments are on could cause an error
  * The -c (or --fullcheck) option in lineage was not declared hence didn't work...
  * ae_individual::reevaluate( ae_environment* envir ) didn't reset the (new) attributes _transcribed, _translated and _folded yielding a flat fitness.
  * In post-treatments that deleted ae_common::sim, ae_dna::undergo_this_mutation( ae_mutation * mut ) could check whether it had to write in the BARRIER log. It hence tried to access a member of ae_common::sim that was NULL.
  * LOADS and BARRIER logs now work correctly
  * There were some inconsistencies with Whole Genome Events (i.e. Whole Genome Duplications)
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