Fix listFilesRecursivelySortByDateOldestFirst

Fails with comparator inconsistency occassionally. Possible causes: live
files updating modification time during the sort or long overflow bug in
Apache Commons library comparator implementation. Fixed both.
Store header length instead of header terminator string
Merge branch 'master' of https://github.com/chipster/chipster.git
Fix manual dataset filtering for GTF and headerless BED
Remove old code row
Add getHeader() method to TableColumnProvider
Add tophat2 update to install and update scripts
Merge branch 'master' of https://github.com/chipster/chipster.git
Affy hta-2.0 added to affy-gene. Hta-2.0 added to affy-exon, but users
cannot yet choose this option.
some mods to hta2.0 additions
Copy a file header when saving selected rows
Interrupt genome browser initialization if an exception occurs
Merge branch 'master' into data_beta

Conflicts:
	src/main/java/fi/csc/microarray/client/selection/IntegratedSelectionManager.java
	src/main/java/fi/csc/microarray/databeans/DataFolder.java
	src/main/java/fi/csc/microarray/databeans/features/table/TableColumnProvider.java
	src/main/java/fi/csc/microarray/module/basic/BasicModule.java