Use of qui

Question

Eg. Tout ce qu’il fait m’agace. Ithought that qui was not shortened before a vowel and it would be ´Tout ce qui il fait m’agace,

Accepted Answer

You are correct in that "qui" is never shortened to "qu' " before a vowel. 
In the sentence you quote, it is actually "que" that got shortened. It can't be "qui" because "qui" is used only for the subject of the subordinate clause. In the case at hand, the subject is "il" and "ce que" is the direct object. Here is an example:
Tout ce qu'il fait m'agace. Everything that he does annoys me.Ils me demandent ce qui m'intéresse. They ask me what interests me.
There are some dedicated exercises right here: https://www.einfranzose.de/grammatik-%C3%BCbungen/pronomen/ce-que-oder-ce-qui.html?sp=de&katid=199 
Hope that helps,
-- Chris (not a native speaker).

Answer

Bonjour Jilly !
To complete Chris's great answer, here are the links to our dedicated lessons on ce qui versus ce que:
https://french.kwiziq.com/revision/grammar/ce-que-what-which-relative-pronouns
https://french.kwiziq.com/revision/grammar/ce-qui-what-which-relative-pronouns
Bonne journée !