SSL: can't load CA certificate file /absolute/path/to/cacert.pem

That message is being thrown from curl, I believe. Are you setting an environmental variable for the CA cert somewhere? Try env | grep cacert.

I am not sure what a environmental variable is. I ran grep cacert and nothing happens and when I run env it just displays a list of information. Sorry I feel clueless on these errors. Do I have to create a CA cert? Where does it come from? I have tired google and not look on this error or what it even is.

env prints out a full list of everything loaded into the environment. Includes your $PATH, $SHELL, any variable you've exported, etc. You shouldn't be seeing this error at all. The error message suggests that somewhere the default example path for a CA certificate from curl is being passed when it shouldn't be.

Make sure you ran the env | grep cacert command whole, not both separately.

Do you have a .bashrc or .zshrc or .bash_profile in your $HOME directory?

Well I think the problem is I don't have a cert to clone from git I always use ssh. Where do I setup a cert to clone from git? I tired to make a .pem file and run git config --system http.sslCAInfo /path/to/file/Certificates.pem but it throws could not lock config file.

You shouldn't need to do any cert-related configuration for this to work. OS X ships with CA certificates already installed, and the system curl set up to respect them. (It's not done with PEM files in newer versions; since 10.9, curl is linked to Apple's Secure Transport framework and gets its CA certs from the system keychain.)

This looks like it might be a problem with the git configuration file, and not environment variables. Since Mavericks, curl doesn't seem to respect the $CURL_CA_BUNDLE environment variable. And I can't induce this error on Mavericks at all. But on El Capitan, I can reproduce this issue by adding the following section to ~/.gitconfig.

[http]
        sslVerify = true
        sslCAinfo = /absolute/path/to/cacert.pem

This reproduces the exact error message when running git (which I believe is calling out to curl or libcurl behind the scenes, like DomT4 suggests, and is passing --cacert or its equivalent).

$ git clone https://github.com/homebrew/homebrew.git
Cloning into 'homebrew'...
fatal: unable to access 'https://github.com/homebrew/homebrew.git/': SSL: can't load CA certificate file /absolute/path/to/cacert.pem

That seems consistent with the OS X curl changes for 10.9 and 10.10.

So, check your ~/.gitconfig for that sslCAInfo line and correct or remove it. Maybe it got edited at some point when you were setting up a git connection to a different server?

Closing as dead. Will reopen or let another maintainer reopen if we get a reply here.