pulledpork re-organizing rules?

["Billy Marshall" <Billy.Marshall () state co us>]

Hi all,
I noticed that Pulled_Pork v0.4.2 is writing the rules to two large files now so there are only 2 rule files;
snort.rules and so_rules.rules
 
Doesn't this defeat the organization of the rules that snort.org has set forth? 
Why is a third party support application re-structuring rule sets and not conforming to snort?
Have I misunderstood something? 
Is snort restructuring its configuration file?
 
With pulledpork:
I can not exclude a rule set with the snort.conf without running pulledpork.
The files snort.rules and so_rules.rules are not in the snort.conf file. If I add them (logically) I will have 
duplicate rules unless I comment out the rules I want to keep that are organized. However, when I really do add the 
files, snort.rules and so_rules.rules , Snort does not initialize.
Furthermore; logically, when I do update with pulledpork and if I was unaware of the changes I would never get the new 
rules because they are stuffed in files that are never looked at by the snort engine without adding them to the 
snort.conf file. 
This is confusing, poses many future issues, and forces snort being dependent on pulledpork.
If I remove all rules from the rules directory and run pulled pork it only creates the afore mentioned files and none 
of the others.
 
<excerpt form pulledpork.conf>
"# What path you want the .rules file containing all of the processed
# rules? (this value has changed as of 0.4.0, previously we copied
# all of the rules, now we are creating a single large rules file
# but still keeping a separate file for your so_rules!
rule_path=/etc/snort/rules/snort.rules
...
s0_rule_path=/etc/snort/rules/so_rules.rules"

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