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[clangd] Filter out plugin related flags and move all commandline manipulations…

Description

[clangd] Filter out plugin related flags and move all commandline manipulations into OverlayCDB.

Summary:
Some projects make use of clang plugins when building, but clangd is
not aware of those plugins therefore can't work with the same compile command
arguments.

There were multiple places clangd performed commandline manipulations,
this one also moves them all into OverlayCDB.

Reviewers: ilya-biryukov

Subscribers: klimek, sammccall, ioeric, MaskRay, jkorous, arphaman, cfe-commits

Differential Revision: https://reviews.llvm.org/D56841