Makefiles: consistently offer `allopt` and `opt.opt` targets

This commit renames a few C compiler related build variables so that
they are reserved for the build system. They will then be re-introduced,
but this time as user varialbes whose value can be freely customized
when compiling the package, without risking to conflict with those
command-line flags that are required by the build system itself.

Here are the variables this commit renames:

- CFLAGS -> OC_CFLAGS
- CPPFLAGS -> OC_CPPFLAGS
- LDFLAGS -> OC_LDFLAGS

Note: before this commit the compilation of scheduler.c in
otherlibs/threads was relying on make's implicit rule to compile C files.

Since this commit stops using the standard variables for flags,
it is necessary to introduce an explicit rule to compile C files
and that makes use of the newly introduced variables.

Some makefiles (lex, stdlib, otherlibs) would only offer allopt, while
others (ocamldoc, tools) only offered opt.opt. It is inconvenient to
have to remember which target name to use while going through various
repositories.

This tool is used to compile ocamlc. Given that make_opcodes is itself
recompiled as part of the bootstrap process, it needs to be run on the new
(rather than old) runtime. In other words, make_opcodes needs to be run
using byterun/ocamlrun rather than boot/ocamlrun.

This commit fixes this.

In environments where the executables compiled to native code,
such as ocamlopt.opt, are always used in preference to the bytecode
versions then space can be saved by not installing the latter.
This patch provides a configure option to do such. It is relatively lightly
engineered; in particular, it won't complain if the native code executables
aren't themselves being built; but given this is an option for knowledgeable
users we think that it is reasonable.