Big Windows compatibility fixes. Now all tests pass in Linux AND Windows!!!
Almost every bug was caused because Perl in Windows hide the '\r' character
from the user when reading the line in text mode, so text length()
is 1 less than the byte length for '\r\n' files, which caused trouble
when the code relied on the byte position of 'tell' and 'seek'.
Now the code check this situation and apply a correction if necessary.
Untabified 't/LocalDB/Index/Index.t' and deleted some empty lines at the
end of a few test files
Bio/SimpleAlign.pm: Fixed a TODO, allowed the use of mask characters
in 'slice'. Related to Bug #2842.