Print orphaned packages in pkg version when comparing with the INDEX file.

They are printed when comparing with the ports tree or the remote
catalogue, so make it consistent.
Remove unused code
Name is the unicity
Fix pkg upgrade leaving directories behind

Fixes:	#1085
Remove unused vars
The mtree is dead since pkg 1.3, remove now useless code
Plug memory leaks
Improve error message, plug memory leak and simplify code
Add documentation for -I
Case-sensitive description was wrong
Add periods for consistency
Return an error on pkg create when adding files
Explicitly send warnings on unexpected syntaxes on manifest

Fixes: #775
Add a test case showing issue with package split
Load repository from a given dir ordered by filename

Fixes: #1020
Inform user about integritycheck issues.
Bring back fetching in the the cache directory for file://

A better solution to prevent that will be added, this allows correctness of integrity checking
Ignore what is no stdout, not the exit number
Prevent dying on duplicated names when upgrading from pkg 1.3

Some databases may be old and may have duplicate package names which is
now forbidden. When upgrading from pkg 1.3 db make sure those names if
any are renamed to be uniq.
Fix pkg fetch -o
Do not return 0 if fetch fails

Reported by:	kmoore
1.4.0 RC1