Missing files in folder tree

[sergiys]

Some files missing in folder tree even after Sublime restart and Project->Refresh Folders. See picture

Sublime Text 3, Build 3126

[wbond]

.exe files are hidden by default via the file_exclude_patterns setting.

[OdatNurd]

By default, directories that are known to house source control information and various binary output files are automatically excluded from the sidebar. If you want to alter that, you can select Sublime Text > Preferences > Settings from the menu (It’s just Preferences > Settings if you’re not on MacOS), and update the following settings from their default values, which are the ones shown here:

    // folder_exclude_patterns and file_exclude_patterns control which files
    // are listed in folders on the side bar. These can also be set on a per-
    // project basis.
    "folder_exclude_patterns": [".svn", ".git", ".hg", "CVS"],
    "file_exclude_patterns": ["*.pyc", "*.pyo", "*.exe", "*.dll", "*.obj","*.o", "*.a", "*.lib", "*.so", "*.dylib", "*.ncb", "*.sdf", "*.suo", "*.pdb", "*.idb", ".DS_Store", "*.class", "*.psd", "*.db", "*.sublime-workspace"],

    // These files will still show up in the side bar, but won't be included in
    // Goto Anything or Find in Files
    "binary_file_patterns": ["*.jpg", "*.jpeg", "*.png", "*.gif", "*.ttf", "*.tga", "*.dds", "*.ico", "*.eot", "*.pdf", "*.swf", "*.jar", "*.zip"],

In particular, you want to copy at file_exclude_patterns and binary_file_patterns from the defaults to your user preferences, and then remove *.exe from file_exclude_patterns and add it to binary_file_patterns.

As the comments mention, the first of those settings controls what files should be excluded from the sidebar, while the second tells it what files in the sidebar are binary and should not be indexed or otherwise searched. Files that you consider to be binary should be covered in one of the two places, depending on whether you want to see them in the sidebar or not.