diff --git a/SKILL.md b/SKILL.md
index 62ad5c0..d841c8b 100644
--- a/SKILL.md
+++ b/SKILL.md
@@ -112,9 +112,12 @@ whether its frontend reads it:
 ```
 
 Fields:
-- **`bazel_args`** — the extra args aquery must run with to mirror the real
-  build (see [Extract the Bazel action graph](#extract-bazel-graph)). Recorded so
-  the comparison is reproducible; read by the operator, not the diff.
+- **`bazel_args`** — the extra **flags** aquery must run with to mirror the
+  real build (see [Extract the Bazel action graph](#extract-bazel-graph)), e.g.
+  `["--config=release"]` or `["-c", "opt"]`; never a command
+  (`["aquery", "mnemonic(...)", ...]` is wrong). Recorded so the comparison is
+  reproducible; check it with Bazel before running aquery (see
+  [Extract the Bazel action graph](#extract-bazel-graph)).
 - **`target_map`** — `reference_name → bazel_name` for intentionally renamed
   **executables**. Bazel targets are keyed by full label, so the value is
   usually `:name` (e.g. `"bssl": ":bssl"`). Libraries need no mapping.
@@ -261,6 +264,8 @@ instead of being a warning nobody reads.
 >   always point to files that are either stale, or do not exist at all.
 
 ```bash
+# bazel_args, as Bazel parses them; it refuses anything that is not an aquery flag
+python3 -c 'import json,os,sys; os.execvp("bazel", ["bazel", "canonicalize-flags", "--for_command=aquery", "--", *json.load(open(sys.argv[1])).get("bazel_args", [])])' any2bazel.json
 bazel aquery 'mnemonic("CppCompile|ObjcCompile|CppLink|CppArchive", //...)' \
     --features=-compiler_param_file --features=-linker_param_file \
     [--config=<name>] [--copt=... --cxxopt=...] \
diff --git a/scripts/config.py b/scripts/config.py
index fd17cbd..cd52739 100644
--- a/scripts/config.py
+++ b/scripts/config.py
@@ -100,9 +100,11 @@ class MigrationConfig:
     # Unlike `ignore` (flags/defines), this is the only lever for missing_tu /
     # missing_target on whole subtrees. Each entry is a reviewable decision.
     exclude_targets: Set[str] = field(default_factory=set)
-    # The bazel aquery invocation this migration is compared against, recorded
-    # so the comparison is reproducible. Read by the skill/operator, not by the
-    # diff itself (the diff consumes the already-extracted model).
+    # The FLAGS appended to `bazel aquery` so the Bazel side mirrors the real
+    # build (never the command itself), recorded so the comparison is
+    # reproducible. Read by the skill/operator, not by the diff itself (the
+    # diff consumes the already-extracted model); SKILL.md has Bazel parse
+    # them before aquery.
     bazel_args: tuple = ()
     # Opt-in: also diff TEST targets (role=test). OFF by default because test
     # diffing requires BOTH models to be extracted with tests enabled and the