improve script to use intermediate file

Scripts will first output results to a temporary file then copy the
results before completion. If the copy fails the script bail with
exit 1.

	modified:   scripts/coge2bed.pl
	modified:   scripts/coge_gff.pl
	modified:   scripts/export_NCBI_TBL.pl
rename CoGe::Tasks packages

Move packages from CoGe::Tasks to CoGe::Pipelines::Misc.

	new file:   modules/Algos/Makefile.PL
	modified:   modules/MANIFEST
	new file:   modules/Pipelines/Makefile.PL
	new file:   modules/Pipelines/Misc/MANIFEST
	new file:   modules/Pipelines/Misc/Makefile.PL
	renamed:    modules/lib/CoGe/Tasks/Genome/Bed.pm -> modules/Pipelines/Misc/lib/CoGe/Pipelines/Misc/Bed.pm
	renamed:    modules/lib/CoGe/Tasks/Genome/Copy.pm -> modules/Pipelines/Misc/lib/CoGe/Pipelines/Misc/Copy.pm
	renamed:    modules/lib/CoGe/Tasks/Genome/Features.pm -> modules/Pipelines/Misc/lib/CoGe/Pipelines/Misc/Features.pm
	renamed:    modules/lib/CoGe/Tasks/Genome/Gff.pm -> modules/Pipelines/Misc/lib/CoGe/Pipelines/Misc/Gff.pm
	renamed:    modules/lib/CoGe/Tasks/Genome/Tbl.pm -> modules/Pipelines/Misc/lib/CoGe/Pipelines/Misc/Tbl.pm
	modified:   web/GenomeInfo.pl
ignore data and cfg files

	modified:   .gitignore