lib dependencies not calculated correctly if src_dir is changed

[Spongman]

Configuration

Operating system:
win10

PlatformIO Version (platformio --version):
PlatformIO, version 3.3.0

Description of problem

platformio doesn't find references to built-in libraries if the src_dir is changed.

Steps to Reproduce

1. set src_dir = .
2. in ./Foo.ino: #include <SPI.h>
3. build

Actual Results

..../Foo.ino:2:17: fatal error: SPI.h: No such file or directory

If problems with PlatformIO Build System:

The content of platformio.ini:

[platformio]
src_dir = .

Source file to reproduce issue:

// Foo.ino
#include <SPI.h>

Additional info

[ivankravets]

Thanks a lot for the report!