Merge pull request #257 from holtgrewe/hotfix/store_swap

[FIX] Fixing swap() for FragmentStore.
Merge pull request #266 from weese/hotfix/static-linkage

Enabled static linkage of libstdc++ and libgcc for apps (master, apply after develop)
[FEATURE,TEST] Adding a new, updated realignment module including tests.
[DOC,NOP] Adding dox documentation, whitespace cleanup.
[INTERNAL] Refactorization of realign helper functions.
[DOX] Adding deprecation message to old reAlign() function.

Includes a fix such that links in @deprecated etc. are also translated.
[INTERNAL] Marking non-public functions and classes with underscores.
[COMMENT] Adding a TODO comment in realignment.
Merge pull request #269 from holtgrewe/feature/realignment

[FEATURE,TEST] Adding a new, updated realignment module including tests.
[FIX] changed hash->std::hash, explicit cast
Merge pull request #276 from weese/feature/fix-bam-scanner

[FIX] removed compile errors of bam scanner
[DOC] Adding @headerfile for function reAlignment().
[FEATURE] add samcat app for concatenation and conversion of SAM/BAM files
[FIX] replaced CharString by std::string
[FIX] registered samcat for KNIME and test system
[FIX] cosmetics
[FIX] Fixing mason2 on Windows

The fix looks quite esoteric and I think that the problem is also a bit esoteric.
I am not sure yet whether we did something wrong in SeqAn, or the MSVC optimizer
is a bit too harsh in is optimization.  In any case, it appears to be related to
using seqan::maxValue<int>() instead of seqan::MaxValue<int>::VALUE.  Note that
we do not have to replace all occurences but one is enough for each int and unsigned.
Merge pull request #286 from holtgrewe/hotfix/mason2_vs

[FIX] Fixing mason2 on Windows
[FIX] Fixing MSA with equal sequences.

Should fix #283 in upstream.
Merge pull request #287 from holtgrewe/hotfix/msa_equal_seqs

[FIX] Fixing MSA with equal sequences.