Bufixes and code reorganization.

* Makefile completely rewritten
* src/main.cpp moved to src/lsg/lsg.cpp
* src/reconstruct_gsa.cpp moved to src/bgsa/bgsa.cpp
* Added reads classifier in src/rdclss/rdclss.cpp
* In search.{h,cpp} added build_tau_interval for Q-Intervals (used in rdclss)
* Defined QIntervalManager as IntervalManager< QInterval >
* Removed TAU and CYCNUM as define in src/types.h
* lsg now accepts -T (--TAU) as parameter
* lsg now accepts -C (--CycNum) as parameter
* Commented out graph print in lsg