Puppet users - Apr 2014 - My dynamic config-file environment broke in 3.5

Hi,

After I upgraded my puppetmaster to 3.5, my clients can no longer find my 
modules. I had my modules broken up into three directories

* modules: third-party modules I install via r10k
* lib-modules: library/generic modules I wrote
* app-modules: application/wrapper modules I wrote

I expressed this in puppet.conf with

[master]
    environment = production
    manifest    = $confdir/environments/$environment/manifests/site.pp
    modulepath  = 
$confdir/environments/$environment/modules:$confdir/environments/$environment/lib-modules:$confdir/environments/$environment/app-modules

However, my puppet runs fail with "Could not find class atop"; that
class
is in lib-modules. When I check the modulepath on my master I don't get 
what I expect

$ sudo puppet config print modulepath --section master --environment 
production
/etc/puppet/environments/production/modules:/etc/puppet/modules:/usr/share/puppet/modules

Based on the documentation I've read [0], I think this is because I named 
the directory that I stored my dynamic environments in "environments".
In
3.5 if puppet sees a directory named "environments" it will use
"directory
environments" instead of "config-file environments". I.E. the
precedence is

static config-file environments → directory environments → dynamic (
$environment) config-file environments

This is a surprise, since I did not intentionally set up directory 
environments and they don't support my modulepath. To me it seems like this 
behavior unncecessarily breaks existing puppet setups. Why isn't the 
precedence

static config-file environments → dynamic ($environment) config-file 
environments→ directory environments ?

Also, shouldn't a warning about this be added to the release notes?

[0] 
http://docs.puppetlabs.com/puppet/latest/reference/environments_classic.html#interaction-with-directory-environments

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