Fixes to hypergraph and htk outputs, better cmd line help.

Mixing boost paths and strings is bad.
Leaks in htk output.
assert that should be an exception
Merge branch 'master' of github.com:moses-smt/mosesdecoder
Added utilities:
- mam2symal converts memory-mapped word alignments to symal format
- mam_verify performs a sanity check on memory-mapped word alignments
Disabled 'rt' in the header specifications. Didn't work in this branch.
Work in progress.
Routine check-in.
Bug fixes in dynamic phrase tables.
moses_chart: more efficient scope-3 parsing if sentence length < max-chart-span
accidental error in perl script
Merge branch 'master' of github.com:moses-smt/mosesdecoder
moses_chart: implement -output-unknowns option.
Surround locks with WITH_THREADS
Compiler warning
Added program calc-coverage.
Removed some debugging messages.
Moved fill_token_seq to tpt_tokenindex.h.
Added function fill_token_seq.
Bug fix in constructor.
Added program calc-coverage.
Added program calc-coverage.
Bug fix. Added sanity check when adding data to dynamic suffix array.