Fix GCC 16 (trunk) debug build: real bug + dead unused-but-set-variable cleanup (#728)
## Summary
This machine has GCC 12 through GCC 16 (16 is an experimental trunk
build) installed side by side. A survey of the debug library build under
each version found:
- **GCC 12, GCC 13**: build cleanly out of the box.
- **GCC 14, GCC 15**: need the `template-id-cdtor` fix in #723.
- **GCC 16**: needs #723's fix *plus* the changes in this PR.
Building under GCC 16 (with #723's fix applied) surfaced 16 unique
`-Werror` sites — mostly `-Wunused-but-set-variable`, plus two
`-Wmaybe-uninitialized` cases (one of which is a real bug):
1. **Real bug** — `core/chemical/CacheableResidueTypeSets.cc`: the copy
constructor initialized its base class with `CacheableData(*this)`
instead of `CacheableData(other)`, reading from the not-yet-constructed
destination object rather than the fully-constructed source. Harmless
today only because `CacheableData` has no data members of its own; still
wrong and exactly what GCC 16 is right to flag.
2. **False-positive trigger** —
`protocols/simple_moves/MissingDensityToJumpMover.cc`: the default
constructor called `MissingDensityToJumpMover::get_name()` (a qualified
call through `*this`, mid-construction) to build an argument for the
`Mover` base class. `get_name()` just returns a string literal, so it's
passed directly instead — avoids the pattern rather than working around
a compiler quirk.
3. **Dead loop counters** (13 sites across 9 files) — variables
incremented alongside a real loop iterator but never read anywhere:
`EnergyGraph.hh` (`iilag`, 2 of 4 occurrences — the other two are real
array indices and are untouched), `PDBInfo.cc` (`idx`, x2),
`mmtf_writer.cc` (`chainIndex`, `modelIndex`), `md.cc` (`imap`),
`StructureDataFactory.cc` (`cur_chain`), `FoldArchitectMover.cc`
(`count`), `pose_mod.hh` (`current_pos`), `DistanceScoreMover.cc`
(`ct_peaks`), `StructureDependentPeakCalibrator.cc` (`pose_ct`). No
behavior change — removed the tracking, left the actual iteration logic
untouched.
4. **Deliberately-unused, kept** — `SapConstraintHelper.cc`'s `offset`
is tracked "for symmetry" per an existing comment even though never
read. Rather than removing it against that stated intent, added an
explicit `(void)offset;` cast to satisfy the warning.