autogen: Add missing indirection through file cache

Symptom:

```
  rm mlkem/src/native/aarch64/src/arith_native_aarch64.h
  autogen
```

fails with

```
  FileNotFoundError: [Errno 2] No such file or directory: \
     'mlkem/src/native/aarch64/src/arith_native_aarch64.h'
```

Context:

A previous commit has introduced an internal file cache to autogen.
During main operation of autogen, all file read/write operations
should go through this in-memory cache.

Issue:

Two instance of direct FS reads via `open(...)` were overlooked
when this change was introduced, leading to an attempt to load
a file from the file system which only exists in the cache.

This commit fixes this by calling the file cache `read_file()`
operation intead.

Signed-off-by: Hanno Becker <beckphan@amazon.co.uk>

Author: hanno-becker

scripts/autogen

@@ -2247,8 +2247,7 @@ def gen_hol_light_asm():
 def update_via_copy(infile_full, outfile_full, transform=None):
     status_update("copy", f"{infile_full} -> {outfile_full}")
 
-    with open(infile_full, "r") as f:
-        content = f.read()
+    content = read_file(infile_full)
 
     if transform is not None:
         content = transform(content)
@@ -2462,8 +2461,7 @@ def adjust_header_guard_for_filename(content, header_file):
 
 
 def gen_header_guard(header_file):
-    with open(header_file, "r") as f:
-        content = f.read()
+    content = read_file(header_file)
     new_content = adjust_header_guard_for_filename(content, header_file)
     update_file(header_file, new_content)