fix: in rules from imported modules, exclude modified paths from module prefixing

tests/test_module_no_prefixing_modified_paths/Snakefile

@@ -0,0 +1,29 @@
+module module:
+    snakefile: "module/Snakefile"
+    config: config
+
+
+use rule * from module1 as module1_*
+
+
+# provide a prefix for all paths in module2
+module module2:
+    snakefile: "module2/Snakefile"
+    config: config
+    prefix: "module2"
+
+
+use rule * from module2 as module2_*
+
+# overwrite the input to remove the module2 prefix specified above
+use rule b from module2 as module2_b with:
+    input:
+        "test.txt"
+
+
+rule joint_all:
+    input:
+        "test2.txt",
+        "test3.txt",
+        "test4.txt",
+    default_target: True

tests/test_module_no_prefixing_modified_paths/expected-results/module2/test_final.txt

@@ -0,0 +1,2 @@
+test_a
+test_c

tests/test_module_no_prefixing_modified_paths/module1/Snakefile

@@ -0,0 +1,5 @@
+rule a:
+    output:
+        "test.txt"
+    shell:
+        "echo test_a > {output}"

tests/test_module_no_prefixing_modified_paths/module2/Snakefile

@@ -0,0 +1,17 @@
+rule b:
+    output:
+        "test.txt"
+    shell:
+        "echo test_b > {output}"
+
+
+rule c:
+    input:
+        "test.txt"
+    output:
+        "test_final.txt"
+    shell:
+        """
+        cp {input} {output};
+        echo test_c >> {output}
+        """

tests/tests.py

@@ -1390,6 +1390,13 @@ def test_module_complex2():
     run(dpath("test_module_complex2"), dryrun=True)
 
 
+def test_module_no_prefixing_modified_paths():
+    run(
+        dpath(test_module_no_prefixing_modified_paths),
+        targets=["module2/test_final.txt"],
+    )
+
+
 def test_module_with_script():
     run(dpath("test_module_with_script"))