pkg version (relatively) recently began showing ">" for ports that were updated with portupgrade

For example:
[root@kahlua]:[~]# pkg version -v | grep -v =
gettext-0.19.5.1                   >   succeeds index (index has 0.19.4)
gettext-runtime-0.19.5.1           >   succeeds index (index has 0.19.4)
gettext-tools-0.19.5.1             >   succeeds index (index has 0.19.4)
linux_base-c6-6.6_6                >   succeeds index (index has 6.6_5)

after numerous unsuccessful attempts to get pkg to update it's index - with no errors ever being reported, I attempted to rebuild the index with make -C /usr/ports index resulted in syntax errors in the script.

Generating INDEX-8 - please wait../usr/local/bin/php-config: not found
"/usr/ports/Mk/bsd.php.mk", line 156: Malformed conditional (${PHP_VER} == 53)
"/usr/ports/Mk/bsd.php.mk", line 317: Malformed conditional (${PHP_VER} == 55 || ${PHP_VER} == 56)
Error expanding embedded variable.
===> archivers/pear-File_Archive failed
*** Error code 1
1 error


I tracked this error down to the existence of EMPTY  /usr/local/etc/php.conf & /usr/local/etc/php.ini files with corresponding symlinks in /etc

Removing those empty files, and rebuilding the index resolved the errant report from pkg version

****

In my opinion, the mere existence of empty php.conf or .ini files should NOT imply php is installed on the system and should not trigger php scripts to be run or tested.

(e.g. In my case I want those empty files to exist and be attribute locked - even if they are empty and even when php is not installed.)

It's also a bit disappointing that NO ERRORS were being generated for "pkg update" or "pkg update -f". Everything just seemed to be happy - except pkg version was showing "newer ports than indexed" as installed - and newer port releases were not triggering "<" (needs updated) - note: portupgrade was updating ports even though "pkg version" didn't show them as outdated.