Move Build.pm out of Root into an install-specific directory; this will
eventually lead up to factoring as much out of it as possible (and maybe
deprecating it altogether)
Revert "Move Build.pm out of Root into an install-specific directory; this will"

This reverts commit 268b046514e9e4cd7b67f346c524ff04b8a3aa5e.
Fixed bug: too many Ns added by spliced_seq

If sequence of an exon is not found, Spliced_seq should add the number
of Ns corresponding to just that exon.
Add tests for spliced_seq remote sequence handling

Add tests to check that the length of spliced_seq is the same when it
resorts to padding with Ns after failing to locate the remote source
sequence for some exons. Also checks that spliced_seq throws the
appropriate warning. The test throws a warning itself if it cannot
complete the tests e.g. due to lack of Genbank access.
Splicedseq.t: Reorganized new tests to use "-requires_networking"
for online tests, and made a format cleaning
Localize Storable options instead of enabling them globally

Otherwise any external code relying on the Storable defaults will be
rudely (and unsafely!) surprised if a Bio::DB::SeqFeature::Store object
is created in the same process.

I'm not sure if $forgive_me = 1 is strictly necessary, but I'm leaving
it.  It can't hurt too much and may paper over other refs which
Data::Dumper can serialize/inflate but Storable can't.
Let Data::Dumper deparse CODE refs to serialize them, just like Storable

Otherwise they are replaced by sub { "DUMMY" }.
Add tsibley's work to Changes file
Clean up and move to proper spot
(Thomas Sibley): Tell Storable to freeze and thaw CODE refs

By default it won't for security.

This reverts commit 5dd8e967998c8ccc3305c5c41c4c2d6f4b6a3395: "skip
tests if the cloning class used happens to be Storable, see bug #3447".

The failing tests from Redmine issue #3447, t/Seq/Seq.t and
t/SeqTools/SeqUtils.t, pass for me both with and without Clone
available.  I tested using -MDevel::Hide=-from:children,Clone.
Reverting the behavor of the index_dir method to silently do nothing if it doesn't find files to index, making it work with GFF files without fasta again.
Fixing a change to a method name that works (_notes_file doesn't exist, _notes_path does)
Location/Split: Added its own "length" subroutine to
handle more complicated cases like cut by origin locations,
which were returning the whole sequence length
(e.g. "join(161..200,1..5))" returned 200 instead of 45).
For transpliced locations (e.g. "join(16..20,complement(6..10))"),
since exons can even be in different chromosomes, it returns
the sum of the lengths of the individual segments. Added tests.
genbank.pm: in "_read_GenBank_Species", adjusted a regex to
not match 'str.' or 'var.' when deciding if the line belonged
to CLASSIFICATION instead of ORGANISM. This happened with NC_021815,
and 2 other plasmids because unusually long descriptions:
  ORGANISM  Salmonella enterica subsp. enterica serovar Typhimurium var. 5-
            str. CFSAN001921
            Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales;
            Enterobacteriaceae; Salmonella.
fix a warning
spiced_seq() may need LWP
Add to documentation, reorganize code a bit
Merge branch 'master' of github.com:bioperl/bioperl-live

Add to documentation, reorganize code a bit
issue 12: changes to _translate_params that allow quoted option values
fix parsing edge case