Remove sample identities from the repository; document the rule

Datasets may be confidential; sample names and measured unit cells committed to
the repo can leak outside the group working on them. Scrub existing occurrences
and add a "No sample identities in the repository" section to CLAUDE.md
(forbidden: sample/dataset names, internal codes, measured cells tied to a
sample; fine: space group / lattice / twinning descriptors).

- Comments: replace internal dataset codes and protein names with the
  crystallographic situation they illustrate (centred vs pseudo-symmetric,
  holohedral, cubic, F-cubic/hexagonal, ...).
- Docs: same, in the analysis/writer/stream references and example configs.
- Tests: rename sample-named identifiers, TEST_CASE names, file prefixes and
  asserted labels to neutral crystallographic names (e.g. tetragonal_uc);
  behaviour unchanged. Reduce the CrystFEL reference PDB to a bare CRYST1 cell
  file (cell.pdb) and rename the reference data file.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

docs/CPU_DATA_ANALYSIS.md

@@ -604,7 +604,7 @@ A reference dataset (`--reference-mtz`) supplies known intensities for the same
 
 **Fix the space group and cell.** Unless overridden on the command line (`-S` for the space group, `-C` for the cell), the reference's space group is adopted and its cell is used as the soft reference cell — indexing may still drift the cell within tolerance, so a small mismatch between reference and data is absorbed rather than rejected. This applies to both stills and rotation data.
 
-**Resolve the indexing (merohedral) ambiguity.** When the lattice symmetry is higher than the crystal's Laue symmetry (e.g. $P3$, $P4$, $P6$, $C2$), more than one indexing of the same lattice is geometrically valid, and the two solutions produce *different* merged intensities that a self-consistent scale cannot tell apart — only an external reference can. The candidate reindexings are the identity together with the twin-law cosets of the metric symmetry (from the unit-cell metric and the Laue group); each is scored by the intensity correlation $\mathrm{CC}_\mathrm{ref}$ of the reindexed merge against the reference, and the data are re-merged in the best-correlating indexing. The reindex is **metric-preserving** — only the $hkl$ labels change, the cell is unchanged — and it is a no-op for a holohedral crystal, which has no twin laws (e.g. lysozyme, where the lattice and Laue symmetry coincide). For rotation data this is done once, after the space group is determined; the reference is *not* used to scale the rotation merge, which stays self-consistent (its $\mathrm{ISa}$ comes from the data alone). For stills the reference is the per-image scale target of the on-the-fly scaling (§10.2).
+**Resolve the indexing (merohedral) ambiguity.** When the lattice symmetry is higher than the crystal's Laue symmetry (e.g. $P3$, $P4$, $P6$, $C2$), more than one indexing of the same lattice is geometrically valid, and the two solutions produce *different* merged intensities that a self-consistent scale cannot tell apart — only an external reference can. The candidate reindexings are the identity together with the twin-law cosets of the metric symmetry (from the unit-cell metric and the Laue group); each is scored by the intensity correlation $\mathrm{CC}_\mathrm{ref}$ of the reindexed merge against the reference, and the data are re-merged in the best-correlating indexing. The reindex is **metric-preserving** — only the $hkl$ labels change, the cell is unchanged — and it is a no-op for a holohedral crystal, which has no twin laws (the lattice and Laue symmetry coincide). For rotation data this is done once, after the space group is determined; the reference is *not* used to scale the rotation merge, which stays self-consistent (its $\mathrm{ISa}$ comes from the data alone). For stills the reference is the per-image scale target of the on-the-fly scaling (§10.2).
 
 ---
 
@@ -699,4 +699,4 @@ Two maps are formed with the model phases $\varphi_\mathrm{model}$: a $2F_o-F_c$
 The model fixes a definite hand and indexing, but the merged data need not share them, so before comparison the observed reflections are brought into the model's frame.
 
 - **Enantiomorph / screw.** When the data space group is the enantiomorph of the model's (e.g. data $P4_12_12$, model $P4_32_12$; or $P3_1/P3_2$), the two are **indistinguishable from merged intensities** — $|F_\mathrm{calc}|$ is invariant under the change of hand, so R-free cannot choose between them and probing would be meaningless. The hand is therefore taken from the model: the observed reflections are reindexed by the change-of-hand operator into the model's enantiomorph. Only the map phases (the density's hand) depend on this choice.
-- **Indexing (merohedral) ambiguity.** When the crystal has a merohedral ambiguity (§10.9), the observed intensities *do* differ between indexings, and the right one is chosen against the best available reference. **If a reference MTZ was supplied, the data were already reindexed to agree with it** (§10.9 — by the reference-intensity correlation, at the merge stage for rotation data or per image in stills scaling), and model validation keeps that authoritative choice. **Only with a model and no reference** does validation resolve the ambiguity itself, as a fallback: the scaled model is fit to each reindexing of the data (identity plus the twin-law cosets) and the one giving the **lowest R-free** is kept. This matters for a multi-dataset campaign — a single shared reference fixes one indexing convention for every dataset, whereas an independent per-dataset lowest-R-free choice could send borderline datasets to different conventions. A no-op either way for a holohedral crystal (no twin laws), e.g. lysozyme.
+- **Indexing (merohedral) ambiguity.** When the crystal has a merohedral ambiguity (§10.9), the observed intensities *do* differ between indexings, and the right one is chosen against the best available reference. **If a reference MTZ was supplied, the data were already reindexed to agree with it** (§10.9 — by the reference-intensity correlation, at the merge stage for rotation data or per image in stills scaling), and model validation keeps that authoritative choice. **Only with a model and no reference** does validation resolve the ambiguity itself, as a fallback: the scaled model is fit to each reindexing of the data (identity plus the twin-law cosets) and the one giving the **lowest R-free** is kept. This matters for a multi-dataset campaign — a single shared reference fixes one indexing convention for every dataset, whereas an independent per-dataset lowest-R-free choice could send borderline datasets to different conventions. A no-op either way for a holohedral crystal (no twin laws).

docs/IMAGE_STREAM.md

@@ -188,7 +188,7 @@ For every image stream socket, downstream code must send the following message t
 ```json
 {
   "run_number":135,
-  "run_name": "lysozyme_1",
+  "run_name": "sample_1",
   "socket_number": 1,
   "processed_images":250,
   "ok": true
@@ -201,7 +201,7 @@ If not, it is possible to include error message:
 ```json
 {
   "run_number":135,
-  "run_name": "lysozyme_1",
+  "run_name": "sample_1",
   "socket_number": 1,
   "processed_images": 0,
   "ok": false,

docs/JFJOCH_WRITER.md

@@ -108,8 +108,8 @@ For example `header_appendix` of `{"param1": "test1", "param2": ["test1", "test2
   "filename": "dataset_name_data_000001.h5",
   "nimages": 1000,
   "file_number": 0,
-  "sample_name": "lysozyme",
-  "run_name": "lyso_cryo",
+  "sample_name": "my_sample",
+  "run_name": "my_run",
   "run_number": 25,
   "experiment_group": "p00001",
   "beam_x_pxl": 1200,

docs/RUGNUX.md

@@ -71,7 +71,7 @@ Index, integrate, scale and merge a rotation sweep, fully de novo:
 
 ```
 rugnux rotation_master.h5 \
-    -o lyso_rot -N 32 \
+    -o rotation_run -N 32 \
     --scaling-high-resolution 1.4
 ```
 
@@ -114,7 +114,7 @@ then merge against a reference structure:
 
 ```
 rugnux serial_master.h5 \
-    -o lyso_serial -N 32 \
+    -o serial_run -N 32 \
     -X ffbidx -C 79,79,38,90,90,90 -S 96 \
     --spot-sigma 4 \
     -z reference.mtz \