You have lost javascript icon

[alexlime]

No icon_js.tmPreferences file in your repo. So javascript icon is not showing.
And JSON....

[ctf0]

because js & json use the default icons ,check this #3

[alexlime]

I don't understand what you mean... As I wrote before you just need to create a file called icon_js.tmPreferences with:

<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
<plist version="1.0">
<dict>
    <key>scope</key>
    <string>source.js</string>
    <key>settings</key>
    <dict>
        <key>icon</key>
        <string>file_type_js</string>
    </dict>
</dict>
</plist>

And everything will work fine:

And same with JSON...

(I have different theme but I used image and .tmPreferences files from your repo)

[ctf0]

what i meant is ST have a native icon-names.tmpref for those 2 ext ,and u simply create ur icon and name them to the natives ,anyway they are re-added again now to avoid such prob later.