Actually, /etc/cron.d/ is part of Linux Standards Base Core
Specification 4.0.  http://refspecs.linux-foundation.org/LSB_4.0.0/LSB-
Core-generic/LSB-Core-generic/etc.html

Yes, .dpkg-* are ignored for a reason, but that also ignores the LSB FHS.  If 
you installed the lsb packages and expect a Linux Standards Base system, then 
`run-parts --verbose --lsbsysinit /etc/cron.hourly/` 
should accept `org.debian.my.cron.job.sh` and 
`debian.org-cron.job.with.dots.sh` and `job.cron` and other filenames with 
dots.  

http://manpages.ubuntu.com/manpages/trusty/en/man8/run-parts.8.html

       If  the  --lsbsysinit  option  is given, then the names must not end in
       .dpkg-old  or .dpkg-dist or .dpkg-new or .dpkg-tmp, and must belong  to
       one  or more of the following namespaces: the LANANA-assigned namespace
       (^[a-z0-9]+$);   the   LSB   hierarchical   and   reserved   namespaces
       (^_?([a-z0-9_.]+-)+[a-z0-9]+$);  and  the  Debian cron script namespace
       (^[a-zA-Z0-9_-]+$).


http://refspecs.linux-foundation.org/LSB_4.0.0/LSB-Core-generic/LSB-Core-generic/etc.html#FHS-NAME-RULES
-Linux assigned names says to use dns.name.com names when you do not have a 
registered name for a particular project.
http://www.lanana.org/lsbreg/cron/index.html

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https://bugs.launchpad.net/bugs/706565

Title:
  configs with dots in file name not working in /etc/cron.d

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