Fix some bugs in incremental update.

Pkg repo now does not emit manifests for duplicate origins packages.

If we have already up-to-date package in our local repo, remove it
from hash and do not allow duplicate inserts into a hash.

Free items from incremental update hash when either delete a package
from update hash or update it.
Fix an example in pkg-query man page
Merge pull request #561 from renchap/master

Fix an example in pkg-query man page
Show message if exists after a package upgrade

Fixes #557
Reported by:	emaste
Fix ssh support
Do not try to update disabled repositories
Properly reset timeout
Fix malformed database in case pkg update is interrupted

Ignore the malformed failure and rebuild the database from scratch.
Modify get_pragma() for it to be able to not emit errors if emission of
errors is not needed
Let dry_mode auto update the catalogs if -U is not passed

dry_mode will update the catalogs except if -U is not passed to install
or upgrade command or the the user has insufficient access to perform an
update of the database.

Fixes: #559
Only add missing deps if the dependency is not already listed

Reported by:	lme
Add debugging level 4 to sql_exec
No need to obtain any exclusive lock for pkg fetch

This allows to run pkg fetch as a user

Fixes:	#553
Allow to pass custom arguments to the ssh(1) command line
Add debug line (level 1) for ssh://
Do not enforce a width limitation on the yaml lines
By default produced inlined yaml

Introduce a new PKG_MANIFEST_EMIT_PRETTY do output human friendly yaml
In all other case produced a inlined manifest which will allow to be
parsed by a quick parser
Move status printing into a function and rename existing end function
pkg-search: Add missing -Q version support

Reported by:	eadler