Adding to the GIT Index with Sublimerge

.zshrc

function sli () {
  if [ -z "$1" ] || [ "$1" = "-h" ]; then
    echo "sli - Sublimerge add to GIT index"
    echo "Usage:"
    echo "sli [options] {path to file}"
    echo
    echo "Call this function in the root of the GIT working tree after using the custom Sublimerge comparison"
    return 0
  fi
  GIT_FILE="$1"
  TEMP_FILE="/tmp/sublimerge/$1@HEAD"
  git show :"$GIT_FILE" |\
    git diff --no-index -- - "$TEMP_FILE" |\
    sed 's|^diff --git.*$|'"diff --git a/$GIT_FILE b/$GIT_FILE"'|' |\
    sed '/^\(---\|+++\)/s|^\(.\{5\}\).*|\1/'"$GIT_FILE"'|' |\
    git apply --cached --verbose;

  if [ "$?" -gt "0" ]; then
    echo "There were no changes to add to the git index"
  else
    git diff --cached --stat "$GIT_FILE" | cat
  fi
  # rm "$TEMP_FILE" 
}

Custom Comparisons.sublime-settings

{
    "custom_comparisons": [
        /************************************* GIT *************************************/

        /*
         * Custom Git comparison. Displays quick panel with modified files and allows to compare working copy to HEAD to see uncommited changes.
         */
        {
            "name": "Show uncommited changes (index)...", //comparison name
            "requires": "git", //What does it require. Currently 'git', 'svn' 'hg' or null (if doesn't require any of VCS)
            "steps": [ //comparison is divided into steps. You can define more steps when needed.
                {
                    "quick_panel": { //Displays a Quick Panel with given attributes
                        "name": "modified_file", //Quick Panel name. Used to populate a variable 'modified_file' with seleted item value
                        "source": { //Data source
                            "execute": { //Execute a shell command
                                "command": "{config:git_executable_path} status --porcelain --untracked-files=no",
                                "directory": "{sublimerge:repo_root}" //Set a command working directory
                            },
                            "item": { //Single item extractor
                                "regexp": "^\\s+M\\s+\"?(.*?)\"?$", //Regular expression to parse each output line
                                "caption": ["@1"], //Caption is an array. Each item is another line. @n - placeholder for regular expression match
                                "value": "@1" //Value must be a single string
                            },
                            "empty_message": "There are no uncommited changes" //Message to be displayed when data source is empty (no items created)
                        }
                    }
                },
                { //define variables
                    "define": {
                        "right_file": "{sublimerge:repo_root}/{modified_file}",
                        // Custom tmp path including sublimerge so we don't accidentally clobber other tmp files
                        "left_file": "{sublimerge:temp_dir}/sublimerge/{modified_file}@HEAD"
                    }
                },
                {
                    "compare": { //Executes file comparison
                        "execute": { //Execute a shell command. Please note about 'modified_file' variable which we defined in previous step
                            // Note the mkdir
                            "command": "mkdir -p \"{left_file|dirname}\" ;{config:git_executable_path} show :\"./{modified_file}\" > \"{left_file}\"",
                            "directory": "{sublimerge:repo_root}"
                        },
                        "left": { //Left file
                            "file": "{left_file}", //Full file path
                            "temporary": false // Keep tmp left_file so we can add it's difference to the git index
                        },
                        "right": {
                            "file": "{right_file}",
                            "temporary": false //This file is our working copy, so is not temporary
                        }
                    }
                }
            ]
        }
    ]
}

Huh, it's in the Custom Comparisons - User file, however I'd not read the documentation and had copied the custom_comparisons key from the Default file >_<