Shaders that are in Assets folder in an empty project add up a lot of time when building. This was not happening in Unity 5.3 as Shaders were ignored just like other not used file types.

Steps to reproduce:
1. Open attached project.
2. Notice: A scene is completely empty. There is a folder "Resources" that contains some Shaders.
3. Build the project.

Result: It takes around 7 minutes to complete the build on MacBook. On 5.3 it took only 2 minutes.

Reproduced with / Not reproduced with:
(minutes:seconds)

| Standalone | iOS
-------------------------------------------------
Unity 2017.1.0a5 | 6:43 | 17:00
Unity 5.6.0f3 | 6:40 | not tested
Unity 5.5.3f1 | 7:00 | not tested
Unity 5.4.5f1 | 6:50 | not tested
Unity 5.3.7p2 | 2:00 | 1:35

Note:
The issue was not reproduced with 5.3. The difference between 5.3 and 2017.1 is ~5 minutes. However, the real issue appears when building for iOS 5.3the difference is around 15 minutes.