Restore omitted Reactome T4; fix oversized table publishing guard

.gitattributes

@@ -58,3 +58,4 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
 # Video files - compressed
 *.mp4 filter=lfs diff=lfs merge=lfs -text
 *.webm filter=lfs diff=lfs merge=lfs -text
+results/Paper_Experiment_Section/Tables/T4_Reactome_ORA_GSEA.csv filter=lfs diff=lfs merge=lfs -text

PUBLIC_Release_Manifest.json

@@ -431,12 +431,16 @@
       "bytes": 16586
     },
     "src/final_comutation/publish.py": {
-      "sha256": "c9b1732abd8063473660c610b27d5d991c58bdbf62f641a08cf6236b1034dff6",
-      "bytes": 9363
+      "sha256": "e46c615de0ed05aa0c9ab77e345d4b15f542ede4f1b57e6d832964fd1b36d1b7",
+      "bytes": 9485
     },
     "src/final_comutation/therapy.py": {
       "sha256": "ba484ab077850cb00c04f6d9efb3a977da076e89694b813d4b7c2b906c79fb6c",
       "bytes": 95111
+    },
+    "results/Paper_Experiment_Section/Tables/T4_Reactome_ORA_GSEA.csv": {
+      "sha256": "a60fb97a325bed9507bd6c59a5d16fc0efae66dd326e1be67cb74b93a8ac1dd2",
+      "bytes": 75746318
     }
   },
   "no_prior_results_used": true,

results/Paper_Experiment_Section/Tables/T4_Reactome_ORA_GSEA.csv

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:a60fb97a325bed9507bd6c59a5d16fc0efae66dd326e1be67cb74b93a8ac1dd2
+size 75746318

src/final_comutation/publish.py

@@ -43,7 +43,7 @@ def safe_files(root):
             rel=p.relative_to(root)
             if any(x in banned_dirs for x in rel.parts) or p.name in forbidden_names:continue
             if p.suffix.lower() not in allow_suffix or p.name.endswith(('.part','.tmp','.temporary')):continue
-            if p.stat().st_size>40*1024**2:continue
+            if p.stat().st_size>40*1024**2 and p.name!='T4_Reactome_ORA_GSEA.csv':continue
             files[str(rel).replace(os.sep,'/')]=p
     # Also bundle exact executed source, not historical notebook.
     src=Path(__file__).resolve().parent
@@ -112,6 +112,7 @@ def publish_all(root):
     if len(files)<15:raise RuntimeError('Too few finished research files for final release: '+str(len(files)))
     mandatory=('results/Audit/Run_Complete.json','results/Audit/Integrity_Checks.json',
                'results/Paper_Experiment_Section/Table_Index.csv',
+               'results/Paper_Experiment_Section/Tables/T4_Reactome_ORA_GSEA.csv',
                'results/Paper_Experiment_Section/Figure_Index.csv',
                'src/final_comutation/pipeline.py', 'src/final_comutation/core.py')
     missing_required=[name for name in mandatory if name not in files]