Drop median_neighbor_distance from collection aggregation

The scalar was mapped to bed_stats.tssdist, a leftover TSS column that
nothing writes: BedStatsModel has never declared the field, so the value
bedboss computed was discarded by extra="ignore" before insert. count()
returned 0, `if not n: continue` fired, and the key was silently absent
from every scalar_summaries payload since the aggregation was written.

Rather than adding a column, a model field and a migration to wire it up,
drop it. Remove the aggregation entry, the matching key in the
_old_stats_to_scalar_summaries fallback, and the BedSetDistributions
docstring line that pointed readers at it as the replacement for the
neighbor_distances KDE. That line now states the real reason the KDE is not
aggregated: each file's curve is fit over its own log10 range, so bin i means
a different bp value per file.

bed_stats.tssdist is left in place; removing it needs its own migration.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01PRGhWjGiUXFoygd35QsKQ7

Author: sanghoonio

bbconf/models/bedset_models.py

@@ -33,8 +33,9 @@ class BedSetDistributions(BaseModel):
     Dropped (retained in per-file distributions blob, not aggregated):
     - widths_histogram: per-file variable-range bins aren't summable; use
       scalar_summaries.mean_region_width histogram instead
-    - neighbor_distances KDE: per-file within-bedset variance is low; use
-      scalar_summaries.median_neighbor_distance instead
+    - neighbor_distances KDE: each file's KDE is fit over its own log10 range,
+      so bin i means a different bp value per file; no collection-level
+      equivalent yet
     - gc_content KDE: per-file distribution is unimodal; use
       scalar_summaries.gc_content mean instead
     - chromosome_summaries: redundant with region_distribution

bbconf/modules/aggregation.py

@@ -45,15 +45,12 @@ def _ids_array(bed_ids: List[str]):
 LARGE_COLLECTION_WARN_THRESHOLD = 5000
 
 # Scalar columns aggregated into ``scalar_summaries``, as
-# (output key, ORM column) pairs. ``median_neighbor_distance`` is stored in the
-# legacy ``bed_stats.tssdist`` column; it is surfaced under the descriptive key
-# without renaming the underlying database column.
+# (output key, ORM column) pairs.
 _SCALAR_COLUMNS = [
     ("number_of_regions", BedStats.number_of_regions),
     ("mean_region_width", BedStats.mean_region_width),
     ("median_tss_dist", BedStats.median_tss_dist),
     ("gc_content", BedStats.gc_content),
-    ("median_neighbor_distance", BedStats.tssdist),
 ]
 
 # Genomic partition columns aggregated into ``partitions``, as

bbconf/modules/bedsets.py

@@ -731,7 +731,6 @@ def _old_stats_to_scalar_summaries(
         "mean_region_width",
         "median_tss_dist",
         "gc_content",
-        "median_neighbor_distance",
     ]
     result = {}
     for key in scalar_keys: