So I'm using Pentaho CDF and I was having problems setting up my own themes. Seems like I could create content using the local folder but when I tried to change the outer content I hit upon problems. I saw that the temples are split into 2, if you see what I mean, with the outer page wrapper living within the /system/pentaho-cdf folder but I couldn't see where they were. The .xcdf file points to template.html but there isn't a template.html file within the folder... then I noticed that there was a template-dashboard.html file and I started to get a glimmer of what was going on, especially as I looked at other .xcdf files and clocked that some had style elements.
Basically what I discovered was that template.html actually represents template-dashboard.html and if there is a style attribute within the .xcdf file then the value of that attribute corresponds to the naming if the template file such that a style attribute with a value of abc (for example) means that a file named template-dashboard-abc.html within the /system/pentaho-cdf folder is parsed.
Lot's of headaches led to this conclusion but I hope that other people don't run into similar problems... the solution sort of came to me while I was asleep - the cat was trying to wake me up and I was trying to stop asleep by thinking of something that was giving me problems, perhaps not the best approach to trying to get to sleep as the cat got his breakfast early and I went into work very early to try out my hypothesis.