Rename identifiers related to special queue.
Renamed Specialitem to GtSpecialcontext.
Use pointers into queue rather than indices.
Remove unnecesary code which complicated computation.
update sqlite to version 3.8.0.1
Merge pull request #81 from stefan-kurtz/sk

Sk
Merge pull request #82 from gordon/sqlite

update sqlite to version 3.8.0.1
add missing include line
union_find: add reset operation

furthermore comment out rank,
which actually is currently unused
paircmp tool: option to output unit edist
macros for addressing a triangular matrix
more work on randomcodes etc
Merge pull request #83 from ggonnella/h-short

pls merge before big changes happen
Added missing assertion in GtSetSourceVisitor constructor
Merge pull request #84 from standage/master

Added missing assertion in GtSetSourceVisitor constructor
use gt_malloc() where possible
Merge pull request #85 from satta/mallocs

use gt_malloc() where possible
get rid of compiler warning (gcc 4.8.1)
Merge pull request #86 from gordon/master

get rid of compiler warning (gcc 4.8.1)
get rid of compiler warning

char doesn't have to be signed