[dune] Add standard flags everywhere

src/init/boot/dune

src/plugins/aorai/dune

src/plugins/callgraph/dune

src/plugins/constant_propagation/dune

src/plugins/dive/dune

src/plugins/e-acsl/dune

src/plugins/from/dune

src/plugins/from/gui/dune

src/plugins/gui/dune

src/plugins/impact/dune

src/plugins/impact/gui/dune

src/plugins/inout/dune

src/plugins/instantiate/dune

src/plugins/loop_analysis/dune

src/plugins/markdown-report/dune

src/plugins/markdown-report/eva-info/dune

src/plugins/metrics/dune

src/plugins/nonterm/dune

src/plugins/obfuscator/dune

src/plugins/occurrence/dune