It depends on what you mean by "100% puppet controlled." Unless you have gone to some effort to ensure that, Puppet is probably asserting less control than you think.
To start, unless you are using both 'recurse => true' and 'purge => true', Puppet will ignore files in the local tree that do not have corresponding files in the source tree. Even when purging is enabled, individual managed Files can safely be placed in the recursively-managed directory tree. In addition, Puppet will not purge directories themselves (only their contents) unless you also set 'force => true'. Furthermore, the 'recurselimit' setting can be used to limit how much of a directory tree is actually managed; that might be useful to you depending and where you want to put unmanaged files relative to managed ones.
John