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You're comparing three different files, as there are multiple repo/file/augeas resources in your catalog. Note the filenames very carefully in the sections below:
parallels-cloud-server.repo
This failed to update as Augeas couldn't parse the file. If you run Puppet with --debug, it should show the output or run "augtool print /augeas//error"
Warning: Augeas[comment /etc/yum.repos.d//parallels-cloud-server.repo](provider=augeas): Loading failed for one or more files, see debug for /augeas//error output
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Error: /Stage[main]/Profiles::Clrepos/Base::Yumrepo[parallels-cloud-server]/Base::Comment[/etc/yum.repos.d//parallels-cloud-server.repo-puppet-comment]/Augeas[comment /etc/yum.repos.d//parallels-cloud-server.repo]: Could not evaluate: Error sending command 'ins' with params ["#comment", "before", "/files/etc/yum.repos.d//parallels-cloud-server.repo/*[1]"]/Error sending command 'ins' with params ["#comment", "before", "/files/etc/yum.repos.d//parallels-cloud-server.repo/*[1]"]
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The warning is just indicating that the file failed to load, the error would then be expected as the thing it's inserting before doesn't exist.
parallels-cloud-server-updates.repo
Puppet is offering to change the updates repo config, but doesn't appear to be doing so as it's in noop mode.
Notice: Augeas[comment /etc/yum.repos.d//parallels-cloud-server-updates.repo](provider=augeas):
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--- /etc/yum.repos.d/parallels-cloud-server-updates.repo 2014-12-22 17:47:20.208756153 +0100
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+++ /etc/yum.repos.d/parallels-cloud-server-updates.repo.augnew 2015-01-05 17:18:26.302794312 +0100
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@@ -1,3 +1,4 @@
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+##This file is managed by puppet
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[parallels-cloud-server-updates]
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cloudlinux-parallels.repo
Note the different section inside the file, different filename too. Puppet didn't log about this file at all.
root@ip # cat /etc/yum.repos.d/cloudlinux-parallels.repo
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#This file is managed by puppet
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[cl-base]
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