The indention issue you see is caused by the theme using the folder icon as disclosure_button, while Sublime Text provides the folder_icon class for that purpose.
To fix that issue, you can create an overide file in your user package (Packages/User/Cyanide - [name].sublime-theme) with the following content.
{
// http://www.sublimetext.com/docs/3/themes.html
"variables": {
},
"rules": [
{
"class": "disclosure_button_control",
"content_margin": [0,0],
},
// Sidebar group closed
{
"class": "icon_folder",
"content_margin": [8,8],
"layer0.texture": "Theme - Cyanide/Cyanide/centurion-folder-closed.png",
"layer0.tint": [250,47,0],
"layer0.opacity": 1,
"layer0.inner_margin": 0
},
{
"class": "icon_folder",
"parents": [{"class": "tree_row","attributes": ["hover"]}],
"layer0.tint":[250,47,0]
},
{
"class": "icon_folder",
"parents": [{"class": "tree_row","attributes": ["selected"]}]
},
// Sidebar group open
{
"class": "icon_folder",
"attributes": ["expanded"],
"layer0.texture": "Theme - Cyanide/Cyanide/centurion-folder-open.png"
},
{
"class": "icon_folder",
"attributes": ["expanded"],
"parents": [{"class": "tree_row","attributes": ["hover"]}]
},
{
"class": "icon_folder",
"attributes": ["expanded"],
"parents": [{"class": "tree_row","attributes": ["selected"]}],
"layer0.texture": "Theme - Cyanide/Cyanide/centurion-folder-open.png"
},
],
}
Note: the content displayed works with ST 3.2+, only.