Preferences menu -> Settings - Syntax Specific...

bookmarks are shown in the gutter...

yes, see https://www.sublimetext.com/docs/3/color_schemes.html#global_settings-find for how to customize your color scheme

just set `"show_encoding": true, "show_line_endings": true,` in your user preferences

it's not a bug, just remove `*.class` from the `file_exclude_patterns` in the preferences

It looks like ST3 a) prompts to delete folders and b) moves files/folders to trash
if you want to change this behavior, just edit `Packages/Default/side_bar.py`. If you don't have this behavior, remove whatever dodgy sidebar plugins you have installed...

just add `"command": "show_panel", "args": {"panel": "output.exec"}` with the appropriate key to your keybindings

a setting to always show a prompt when a file is modified externally (`always_prompt_for_file_reload`) was added in build 3032