removed all references to seq_fixer in console controller
removed seq_fixer
removed references to filtermanager.dirty from console controller, removed seqfixer tests from alltests
moved lines around so filter.remove gets set before filter.apply gets called; we can flag again
s/apply_filters_n_fixes/remove_empty_features/
stats manager now updated automatically, but no 'modified' results printed if they all match the originals
removed deepcopies, re-added stats_mrg.clear_alt() to console_controller.stats(); oops
console controller has removed features, not just removed seqs. sequence returns list of removed genes upon call
genes return removed mrnas; seqs pass them along too.
console controller removes empty features after filter or fix terminal ns; keeps list of removed features
gene.remove_mrnas_from_list returns removed mrnas
sequence.remove_genes_from_list returns removed genes
sequence.remove_mrnas_from_list returns removed mrnas
console controller.remove from list now updates its removed features
s/will be removed/removed/ in main console messages
Merge branch 'nomodeepcopy' of https://github.com/BrianReallyMany/GAG into nomodeepcopy

Conflicts:
	gag.py
	src/console_controller.py