Consolidate offline tools into rugnux; merge on by default

Fold jfjoch_azint and rugnux_scale into the single rugnux CLI, and flip
scaling/merging from opt-in to on-by-default.

- rugnux --azint-only replaces jfjoch_azint (reuses ProcessMode::
  AzimuthalIntegration; adds the correction toggles and geometry overrides
  the old tool carried).
- rugnux --scale replaces rugnux_scale (re-scale/merge stored reflections,
  same simpler scale/merge as before: no space-group search or rot3d
  defaults). Its workflow is folded into the CLI verbatim.
- Merging is now on by default for rotation and stills; --no-merge disables
  it, replacing -M/--scale-merge.

Also fix the batch ReadReflections reader so it works on rugnux's own
NXmxIntegrated _process.h5: read per-image reflections/mosaicity/lattice
from the master (global index) first, falling back to the source-data
locator for legacy/VDS datasets. Without this, both --scale and the former
rugnux_scale read zero reflections from an integrated snapshot.

RugnuxCommandLine now emits `rugnux --azint-only` and `--no-merge`; docs and
tests updated to match.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

reader/HDF5MetadataSource.cpp

@@ -1102,14 +1102,21 @@ std::vector<IntegrationOutcome> HDF5MetadataSource::ReadReflections(size_t start
         // Generic (non-image-specific) detector geometry from experiment setup.
         outcome.geom = cached_geom;
 
-        // Per-image reflections and MX metadata live in the same file as the image pixels,
-        // at the source-local index (the locator keeps the data-file handle cached).
-        const auto loc = ResolveMeta(static_cast<int64_t>(img));
-        HDF5Object *meta_file = loc.file.get();
-        const size_t meta_image_id = loc.local_index;
+        // Per-image reflections and MX metadata are stored in this master at the global index for a
+        // self-contained integrated _process.h5 snapshot, or co-located with the pixels in the source
+        // data file at the source-local index for a legacy/VDS dataset. Prefer the master (so an
+        // integrated snapshot reads without its linked source data present); fall back to the source.
+        HDF5ReadOnlyFile *meta_file = master_file.get();
+        size_t meta_image_id = img;
+        std::string refl_group = fmt::format("/entry/reflections/image_{:06d}", img);
+        if (!master_file->Exists(refl_group)) {
+            const auto loc = ResolveMeta(static_cast<int64_t>(img));
+            meta_file = loc.file.get();
+            meta_image_id = loc.local_index;
+            refl_group = fmt::format("/entry/reflections/image_{:06d}", meta_image_id);
+        }
 
         // ── reflections ──────────────────────────────────────────────────────
-        const std::string refl_group = fmt::format("/entry/reflections/image_{:06d}", meta_image_id);
         ReadReflectionsFromGroup(*meta_file, refl_group, outcome.reflections);
 
         // ── per-image mosaicity ───────────────────────────────────────────────