fix(docs): cite files, not line numbers, in the generated env reference (#6538)

website/configuration-reference.md pinned every ODYSSEUS_* read to a
`path:line`, and test_env_reference fails when the committed page differs from
the generator output. So any change that adds or removes a line above an env
read in any scanned file has to regenerate the page, even when no variable
changed. Since the page landed on 2026-09-30, 24 of the 34 commits touching it
changed nothing but line numbers, and all three open PRs that touch it today do
the same - which also makes them conflict with each other on that file.

The Read in column now names the file, and "+N more" counts other files rather
than other read sites. The page still goes stale, and the test still fails,
when a variable is added, removed, moves to another file, or changes default.
check_notes still reports path:line on stderr, where it is useful and never
committed.

scripts/generate_env_reference.py

@@ -1023,9 +1023,15 @@ def _cell(text: str) -> str:
 
 
 def _read_cell(variable: Variable) -> str:
-    primary = f"`{variable.primary.location}`"
-    extra = len(variable.reads) - 1
-    return primary if extra <= 0 else f"{primary} (+{extra} more)"
+    """The file a variable is read in, and how many other files read it.
+
+    Files only, never line numbers. A line number here goes stale whenever an
+    unrelated edit shifts the file, which made every such PR regenerate this page
+    and conflict with every other PR doing the same.
+    """
+    primary = variable.primary.path
+    extra = len({read.path for read in variable.reads} - {primary})
+    return f"`{primary}`" if extra <= 0 else f"`{primary}` (+{extra} more)"
 
 
 def _default_cell(variable: Variable) -> str: