Reader: reconstruct the background variance a legacy file does not store

A _process.h5 written before background_variance existed was read with var_bkg = 0, on the reasoning
that zero leaves the combine with the signal term alone, "which is what it had before". It does not.
Before, the combine back-derived the non-signal variance from sigma itself, and on a weak reflection
that is essentially the whole of sigma^2; zero deletes the dominant term and weights the reflection by
roughly 1/I instead of 1/sigma^2.

Recover it from the integrator's own identity, sigma^2 = I + var_bkg, when the dataset is absent.

Measured by re-scaling a stills _process.h5 with the dataset deleted, against the same file with it
intact: the automatic resolution cutoff was reading 1.66 A where the intact file reads 1.81, with
14731 unique reflections against 11508 - i.e. the zeroed file looked good enough to merge 0.15 A past
its own limit. Reconstructed, it reads 1.78 A and 11926, within 0.03 A of the intact file. The
residue is the profile-fit path, where var_bkg is not exactly sigma^2 - I and only the box-sum
identity is exact; that is recoverable to a closer approximation only by storing it, which is what
files written from now on do.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>

reader/HDF5MetadataSource.cpp

@@ -179,9 +179,12 @@ bool ReadReflectionsFromGroup(HDF5Object &file,
         if (zeta.size() > i)
             zeta_val = zeta[i];
 
-        // A file written before the merge carried this cannot say what the non-signal variance was;
-        // 0 leaves the combine with the signal term alone, which is what it had before.
-        float var_bkg_val = 0.0f;
+        // A file written before this dataset existed has to have the non-signal variance reconstructed,
+        // not zeroed. The combine takes var_bkg as the authoritative non-signal term, so a zero would
+        // leave it the signal alone and weight a weak reflection by ~1/I instead of ~1/sigma^2 - orders
+        // of magnitude too high, and worst exactly where the reflection is weakest. The integrator's own
+        // identity sigma^2 = I + var_bkg inverts to recover what the file does not store.
+        float var_bkg_val = std::max(0.0f, int_err.at(i) * int_err.at(i) - int_sum.at(i));
         if (var_bkg.size() > i)
             var_bkg_val = var_bkg[i];