aconfig: modify and filter flags before passing into java codegen

Before this change java codegen filter flags for exported mode in the
template. This change move the filter process to commands as other
codegen. Thus the codegen code will only generate code based on the
passed in flags.

Bug: 311152507
Test: atest aconfig.test aconfig.test.java AconfigJavaHostTest
Change-Id: I74045709cde19e6c687c3eb0d94050ea40cf5042