docs: prune research vault to theory-only scope

Remove gA-extraction notes, nuclear-structure notes, paper-summary
refs, detector-response correction note and the finished test
migration checklist. Rewrite the vault index for the single-package
theory calculator; repoint dangling wiki-links in surviving notes to
inline citations; refresh docs_check.py (drop bs_exp CLI check,
register removed files).

Literature and nuclear-structure research resumes in dedicated
projects; the removed notes are recoverable from history.

scripts/docs_check.py

@@ -176,7 +176,19 @@ def check_file_references(report: Report):
 
     # Known historical references that are intentionally kept in docs
     # (files that were removed as part of a migration/cleanup)
-    known_removed = {"cw_extractor.py", "fitter.py", "test_cw_extractor.py"}
+    known_removed = {
+        "cw_extractor.py",
+        "fitter.py",
+        "test_cw_extractor.py",
+        "detector_response.py",
+        "shape_factor_gA.py",
+        "exp_data",
+        "fitter",
+        "analyze_raw.py",
+        "exp_calibration.ipynb",
+        "exp_cli.py",
+        "recoil.py",
+    }
     # Placeholder examples used in documentation
     known_placeholders = {"foo.py", "test_foo.py"}
 
@@ -258,22 +270,6 @@ def check_cli_commands(report: Report):
         except (subprocess.TimeoutExpired, FileNotFoundError):
             report.add("WARN", "AGENTS.md", "cli", "bs_pnpi not found in PATH")
 
-    # Check bs_exp CLI
-    if "bs_exp" in agents_md:
-        try:
-            result = subprocess.run(
-                ["bs_exp", "--help"], capture_output=True, text=True, timeout=10
-            )
-            if result.returncode != 0:
-                report.add(
-                    "WARN",
-                    "AGENTS.md",
-                    "cli",
-                    f"`bs_exp --help` failed: {result.stderr.strip()[:100]}",
-                )
-        except (subprocess.TimeoutExpired, FileNotFoundError):
-            report.add("WARN", "AGENTS.md", "cli", "bs_exp not found in PATH")
-
 
 def check_imports_in_examples(report: Report):
     """Check that import statements in README examples are valid."""