Fix samples/rot13_concise + libxml compilation error

boehm_gc/.gitignore:
    Ignore .obj files

extras/xml/xml.dtd.m:
extras/xml/xml.parse.m:
    Change the name of functor ('1') in the multiplicity/0 type
    to one. The former name does not (yet) work with the C# grade.

samples/.gitignore:
    Ignore library output and sample executables.

samples/c_interface/standalone_c/.gitignore:
    Ignore mercury_lib_int output files.

samples/c_interface/standalone_c/Makefile:
    chmod 0644.

samples/c_interface/.gitignore:
    Ignore object files and executables.

samples/java_interface/.gitignore:
    Ignore Java class files and executables.

samples/lazy_list/.gitignore:
samples/muz/.gitignore:
samples/rot13/.gitignore:
    Ignore executables.

samples/rot13/rot13_concise.m:
    Update call to index_det to use string.det_index.
    Added comments to clarify type inference.

samples/solutions/.gitignore:
    Ignore executables.

samples/solutions/all_solutions.m:
samples/solutions/n_solutions.m:
samples/solutions/one_solution.m:
samples/solutions/some_solutions.m:
    chmod 0644.

samples/solver_types/.gitignore:
    Ignore executables.

samples/solver_types/sudoku.m:
    Output the solution in a 3x3 grid.
Delete --no-main from COMP_FLAGS.

main.c was deleted in commit 268b6fff783f709e40e4b71b3c2a5cfccafceac9
and --no-main was removed from MLFLAGS, but another instance occurs in
COMP_FLAGS.  The latter only affects the mmc --make build process,
not mmake.

compiler/COMP_FLAGS.in:
	Delete --no-main from COMP_FLAGS to restore compilation
	with mmc --make.
Clearly explain what part of partial instantiation isn't supported.

In (at least) two places we say that partial instantiation doesn't work or
isn't supported.  This has raised confusion so this patch attempts to
explain what exactly is unsupported and why.

doc/reference_manual.texi:
library/list.m:
LIMITATIONS:
    As above.

library/list.m:
    Delete deprecated modes.

    Move partial instantiation states and modes into a private interface
    section.  Note all of the instantiation states are partial, some can be
    safely used for subtyping so I've left those where they are.

LIMITATIONS:
    Include Zoltan's explanation of why this doesn't work for our future
    selves and others.