abyss-map: Map unmapped potions of queries

* Map/map.cc (toXA): New function. Converts a match to an XA tag.
(findMatch): Factored from find.
(find): Attempt to align flanking sequences of the best matching
substring, and append as an XA tag entry for the sam record.
FMIndex/FMIndex.h (Match): Add default constructor to Match.
abyss-map: print XA tag only when matches exist.
abyss-gapfill: New program.
abyss-gapfill: Store alignment tags.
abyss-gapfill: Store the scaffolds and alignments.
abyss-gapfill: Compile with dialign
abyss-gapfill: Overlap and align spanning reads
abyss-gapfill: Code cleanup.

* GapFiller/gapfill.h: Moved definition of Scaffold here.
* GapFiller/gapfill.cpp (Scaffold): Moved some funcitons
to Scaffold scope.
(stats): Added tracking of number of gaps, gaps filled, N's
removed, and bases added.
(alignReadsToGapFlanks): Don't align with dialign. Instead
use alignGlobal instead.
abyss-gapfill: Minor changes to debug output.
abyss-gapfill: gcc47 compiler error fixes.
Only compile abyss-gapfill if samseqqual enabled.
abyss-map: New option --multi.

* Map/map.cc (toXA): Only compile with SAM_SEQ_QUAL
(find): Check for --multi option.
(main): Return error if --multi used and not compiled with
SAM_SEQ_QUAL.
Release 1.3.6
Merge branch master into develop

* master:
  Document verbose logging
abyss-mergepairs: report number of unchaste pairs removed
change gapfill alignment stats counters to unsigned long long, avoid integer overflow
Don't track *.orig files created by git diff.
Check that the Haskell package MMAP is installed.

Closes bcgsc/abyss#29
abyss-map: Set mapq=0 for multiple mappings of same length

* FMIndex/FMIndex.h (Match): New member, num to track number of times
equal matches were found.
(findSubstring): use Match::num.
* Map/map.cc (toSAM): Set mapq=0 when there are multiple best matches.

Fixes the stats for bcgsc/abyss#19 but there are 5 cases where the
number of N's between contigs introduced by Overlap is different.
Removing some whitespace.