Fix API usage errors in geometry tests

Fix API usage errors in geometry tests

Fixes validation errors in various geometry tests.

geometry.basic.output_* tests were potentially exceeding the
maxGeometryTotalOutputComponents limit because the gl_PerVertex was
implicitly declared and therefore contained gl_Position and gl_PointSize.
Now the gl_PerVertex is declared explicitly to contain only gl_Position.

Fixes flush/invalidate mapped memory range -validation errors by using the
flushAlloc/invalidateAlloc -framework functions.

Affects:
dEQP-VK.geometry.basic.output_*
dEQP-VK.geometry.instanced.*

Components: Vulkan

VK-GL-CTS issue: 1911

Change-Id: I8e4cfd5879ba8c61be3019578b8afbc76592d82e