diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index b4dcb51f..db8e2d22 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -8,9 +8,34 @@ repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.5.0
     hooks:
+      # The three hooks below REWRITE files rather than just checking them, so
+      # they must not touch trees we do not author. Without this exclusion a
+      # `pre-commit run --all-files` silently reformats vendored upstream source
+      # and the immutable reference corpus — observed: 41 files across the
+      # vendored TriCNES C#, the vendored rcheevos C, `ref-docs/`, an upstream
+      # font licence, and upstream test-ROM READMEs. That destroys the "kept
+      # pristine / byte-identical to upstream" property those trees exist for,
+      # and pollutes any diff that happens to run the hooks broadly.
+      #
+      # `.markdownlintignore` already exempts most of these for markdownlint;
+      # this is the equivalent for the whitespace fixers, which had no exclusion
+      # at all. Scope is deliberately narrower than `.markdownlintignore`: only
+      # content we did not write (vendored / upstream / immutable reference).
+      # Frozen-but-ours trees (`docs/archive/`, `to-dos/plans/`, …) stay in
+      # scope — they are our prose, and whitespace hygiene on them is harmless.
       - id: trailing-whitespace
         args: [--markdown-linebreak-ext=md]
+        exclude: &vendored_trees |
+          (?x)^(
+            ref-docs/
+            |ref-proj/
+            |crates/rustynes-test-harness/golden/tricnes/
+            |crates/rustynes-cheevos/vendor/
+            |tests/roms/
+            |assets/RustyNES_Icon/OFL\.txt$
+          )
       - id: end-of-file-fixer
+        exclude: *vendored_trees
       - id: check-yaml
         # mkdocs.yml uses Material for MkDocs' documented `!!python/name:` YAML
         # tags (pymdownx.emoji icon rendering), which check-yaml's safe_load
@@ -35,6 +60,9 @@ repos:
       - id: check-merge-conflict
       - id: mixed-line-ending
         args: [--fix=lf]
+        # Third rewriting hook — same exclusion. Upstream `.resx` / `.csproj`
+        # files in the vendored TriCNES tree legitimately carry CRLF.
+        exclude: *vendored_trees
 
   # Markdown linting
   - repo: https://github.com/igorshubovych/markdownlint-cli
diff --git a/scripts/diag/celldiff.py b/scripts/diag/celldiff.py
index fef7e480..50745450 100644
--- a/scripts/diag/celldiff.py
+++ b/scripts/diag/celldiff.py
@@ -45,7 +45,7 @@ def rnorm(acc):
 
 # Walk both from landmark, report first structural divergences (addr or normalized-kind)
 mlist=mes[mi:]; rlist=rny[ri:]
-# Mesen has NO Idle rows; RustyNES emits I rows. To align, drop RustyNES I rows? 
+# Mesen has NO Idle rows; RustyNES emits I rows. To align, drop RustyNES I rows?
 # But I rows ARE cycles. Mesen logs a read every cycle (no idle). So an I in Rusty
 # where Mesen has a read = the structural divergence we hunt. Keep both, align by index.
 divs=0
@@ -57,7 +57,7 @@ def rnorm(acc):
     if ma!=ra or mk2!=rk2:
         print(f"off={off:5d} | MES {mk}{('('+mk+')') if mk in 'HDAG' else ''} {ma:04X}={mv:02X} | RNY {racc} {ra:04X}={rd:02X} indmc={indmc}")
         divs+=1
-        if divs>=40: 
+        if divs>=40:
             print("... (capped at 40)")
             break
 print(f"total divergences shown (cap 40 of first {n} aligned cycles)")