alignment features, PassThroughN features, dtrain update, mira qsub, and pro fix

Hi Chris, here are a bunch of changes I'd like to merge. Nothing invasive, only the PassThroughN features are disabled by default.
Patrick


**decoder/ff_lexical.h**
* Felix' alignment features
  (see also cdec_ff.cc)

**decoder/scfg_translator.cc**
* *add_extra_pass_through_features* parameter for cdec to make PassThroughN features optional
  (see also decoder/decoder.cc)

**training/dtrain/:**
* fixes and additions

**training/mira/mira.py:**
* enable use of qsub
* *verbose* flag to enable/disable excessive output
  (see also training/mira/kbest_cut_mira.cc: excessive mira output)

**training/pro/pro.pl**
* pmem parameter for qsub