How to do negative pattern for VS Code files exclude

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The short answer is No, VS Code have not support it yet. (2016-12-09)

So is this the end ? No

Here is the work around.

files.exclude
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"files.exclude": {
   "**/node_modules": false,
   "**/node_modules/.*": true,
   // hide all folders that doesn't start with letter 'a'
   "**/node_modules/[bcdefghijklmnopqrstuvwxyz]*": true,
   // hide all folders that doesn't start with 'ap'
   "**/node_modules/a[abcdefghijklmnoqrstuvwxyz]*": true
 }

Kudos to 1-9@Github