fix phase offset handling during sequence extraction

Closes #447.
add additional test case for phase offset
Merge pull request #448 from satta/phases

fix phase offsets for sequence extraction
add some scripts
cosmetics, review TODO/XXX add DW label to them
add condenser testdata
fix and improvement for intset

searching for a number > as the largest in the set resulted in an error.
this is not as intended, it should return the number of elements in that
case.
refactoring addition of new method

this adds a new filtering aproach to the hit finding in the compression
phase of condenser
add hint about file name list termination
streamline/update example filter function
Merge pull request #450 from Garonenur/condenser

Condenser
Merge pull request #453 from satta/filename_term

Improve documentation of 'gt select'
fix typo
update generated website
add FISH Oracle 2 paper to GenomeTools website
gth: new option -cdnaforward
use correct format specifier
add pre-commit script asking for confirmation when APIs are changed
Merge pull request #455 from gordon/www

add FISH Oracle 2 paper to GenomeTools website
Merge pull request #458 from satta/api_precommit

add pre-commit script asking for confirmation when APIs are changed