UPDATE:
Master pages are quite useful. Use them when applicable, but pay careful attention when you have thousands of lines of legacy javascript. I will leave the original post as is…this is a learning experience for me as well. Note my frustration below:
/UPDATE
UPDATE 2:
Paragraph 2 doesn’t make any sense to people that were not working on that project. I should have made this much more generic
/UPDATE 2
My suggestion: don’t use Master Pages. That is, until MS releases a tool to retrofit your existing javascripts or prevent master pages from name mangling. From what I hear, it is hell on CSS as well, but I haven’t run into that yet.
Instead, I just created 2 user controls, one containing the head of my layout, and one containing the footer. Simple enough for me, and I don’t have to waste time figuring out why my scripts don’t work. If that’s not good enough for you, you’ll need to make use of the .clientID property in your code behind pages – it just was not a viable option in my particular case.