Ensure both generated and manual patches affect spec generation

Previous to this change, if there were no manual changes, the automatically
generated patch would not affect the calculated metadata, and result in
broken .spec files.

rust2rpm/__main__.py

@@ -272,21 +272,32 @@ def make_patches(args, version, toml):
     diff1 = diff2 = None
     toml_path = f"{args.crate}-{version}/Cargo.toml"
 
-    # We always do the automatic part before asking the user for more edits.
-    if toml_after := args.patch_foreign and drop_foreign_dependencies(toml_before):
-        diff1 = make_diff(toml_path, toml_before, mtime_before, toml_after, mtime_before)
-    else:
-        toml_after = toml_before
+    # patching Cargo.toml involves multiple steps:
+    #
+    # 1) attempt to automatically drop "foreign" dependencies
+    #    If this succeeded, remove the original Cargo.toml file, write the
+    #    changed contents back to disk, and generate a diff.
+    # 2) if requested, open Cargo.toml in an editor for further, manual changes
+    #
+    # The changes from *both* steps must be reflected in the Cargo.toml file
+    # that ends up on disk after this function returns. Otherwise, the
+    # calculated metadata and generated spec file will not reflect the patches
+    # to Cargo.toml that were generated here.
 
-    if args.patch:
+    if toml_after := args.patch_foreign and drop_foreign_dependencies(toml_before):
         # remove original Cargo.toml file
         os.remove(toml)
 
         # write auto-patched Cargo.toml to disk
         with open(toml, "w") as file:
             file.writelines(toml_after)
-            file.flush()
 
+        diff1 = make_diff(toml_path, toml_before, mtime_before, toml_after, mtime_before)
+    else:
+        toml_after = toml_before
+
+    if args.patch:
+        # open editor for Cargo.toml
         editor = util.detect_editor()
         subprocess.check_call([editor, toml])
 

rust2rpm/cfg.py

@@ -116,8 +116,9 @@ def evaluate_atom(name: str) -> bool:
             return False
         case _:
             log.warn(
-                f"Ignoring invalid atom {name!r} in cfg-expression. "
-                + 'Only "unix" and "windows" are valid names for atoms.'
+                f"Ignoring unknown identifier {name!r} in cfg-expression. "
+                + 'Only "unix" and "windows" are standard identifiers, '
+                + 'any non-standard "--cfg" flags are not supported.'
             )
             return False