Update webupdate and webupdate.wrapper to fix several issues.

In webupdate:

• Output the ports tree checkout to the log file.
• Set the depth of ports/Mk/ to 'infinity', since its contents are needed for 'fetchindex' to work properly.
• Reduce redundant explicit paths to use the value of 'subdirs'.

In webupdate.wrapper:

• Set PORTSDIR to the actual path that is being updated by webupdate.
• If PINDEX_OVERRIDE is set, remove the INDEX-INDEXNUM file.

Approved by: doceng (implicit)
Sponsored by: The FreeBSD Foundation