Provide MMDB Shim built on gemmi

[Dialpuri]

Replace MMDB2 with a gemmi-backed shim

Coot can now be built against mmdb-shim/ instead of libmmdb2. The shim presents
MMDB's public API (mmdb::*) unchanged, but every object is a thin wrapper over
a live gemmi::Structure. Goal: drop the MMDB2 dependency while keeping MMDB's
observable behaviour.

Status: the full Coot tree compiles and links against the shim, and the
shim's own test suite passes. Runtime validation against real structures is still
required.

What's here

• The shim (mmdb-shim/): mostly header-only inline implementations
  over gemmi, plus a compiled component (src/contacts.cc, src/io.cc) built
  into libmmdbshim.a. It uses gemmi for the real work (I/O, symmetry, neighbour
  search, mmCIF) and reimplements the parts gemmi lacks (MMDB's selection engine
  and UDData). Public headers fall through to real MMDB when COOT_USE_MMDB_SHIM
  is off. See mmdb-shim/ARCHITECTURE.md for the full design.
• A one-time source rewrite (~181 files): MMDB exposes atom/residue fields as
  public data members, which gemmi can't; a clang AST-matcher tool converted
  field access to accessors (atom->x → atom->x(), strcpy(at->name,…) →
  at->SetAtomName(…)).

Build

Coot builds against the shim via the CMake path; the shim's tests build with
mmdb-shim/build.sh.