diff --git a/src/main/java/net/md_5/specialsource/JarMapping.java b/src/main/java/net/md_5/specialsource/JarMapping.java
index f1f521e..3d9b43d 100644
--- a/src/main/java/net/md_5/specialsource/JarMapping.java
+++ b/src/main/java/net/md_5/specialsource/JarMapping.java
@@ -93,45 +93,6 @@ public class JarMapping {
         return mapped;
     }
 
-    /**
-     * Load mappings given a (path) specification, optionally:
-     * - reversed through a prefix '^'
-     * - relocated through a suffix '@oldpath1=newpath1,oldpath2=newpath2'...
-     *
-     * Intended for convenient command-line usage.
-     */
-    public void loadMappings(String spec) throws IOException {
-        boolean reverse;
-
-        if (spec.startsWith("^")) {
-            reverse = true;
-            spec = spec.substring(1);
-        } else {
-            reverse = false;
-        }
-
-        if ((new File(spec)).isDirectory()) {
-            loadMappingsDir((new File(spec)), reverse);
-            return;
-        }
-
-        int n = spec.lastIndexOf('@');
-        String path;
-        JarMappingLoadTransformer inputTransformer;
-
-        if (n == -1) {
-            path = spec;
-            inputTransformer = null;
-        } else {
-            path = spec.substring(0, n);
-            inputTransformer = new ShadeRelocationSimulator(spec.substring(n + 1));
-        }
-
-        BufferedReader reader = new BufferedReader(new FileReader(path));
-
-        loadMappings(reader, inputTransformer, null, reverse);
-    }
-
     /**
      * Load mappings from an MCP directory
      */
diff --git a/src/main/java/net/md_5/specialsource/SpecialSource.java b/src/main/java/net/md_5/specialsource/SpecialSource.java
index 7bbe5f4..e71c75a 100644
--- a/src/main/java/net/md_5/specialsource/SpecialSource.java
+++ b/src/main/java/net/md_5/specialsource/SpecialSource.java
@@ -69,9 +69,18 @@ public class SpecialSource {
 
                 acceptsAll(asList("m", "srg-in"), "Mapping file input")
                         .withRequiredArg()
-                        .describedAs("path[@relocations...]")
                         .ofType(String.class);
 
+                acceptsAll(asList("R", "in-shade-relocation", "shade-relocation"), "Simulate maven-shade-plugin relocation patterns on srg-in input names")
+                        .withRequiredArg()
+                        .withValuesSeparatedBy(',');
+
+                acceptsAll(asList("out-shade-relocation"), "Simulate maven-shade-plugin relocation patterns on srg-in output names")
+                        .withRequiredArg()
+                        .withValuesSeparatedBy(',');
+
+                acceptsAll(asList("r", "reverse"), "Reverse input/output names on srg-in");
+
                 acceptsAll(asList("i", "in-jar"), "Input jar to remap")
                         .withRequiredArg()
                         .ofType(File.class);
@@ -80,10 +89,6 @@ public class SpecialSource {
                         .withRequiredArg()
                         .ofType(File.class);
 
-                acceptsAll(asList("R", "shade-relocation"), "Simulate maven-shade-plugin relocation patterns on srg-in")
-                        .withRequiredArg()
-                        .withValuesSeparatedBy(',');
-
                 acceptsAll(asList("l", "live"), "Enable runtime inheritance lookup");
                 acceptsAll(asList("L", "live-remapped"), "Enable runtime inheritance lookup through a mapping");
 
@@ -136,19 +141,37 @@ public class SpecialSource {
 
             jarMapping = new JarMapping();
 
+            // Optional shade relocation, on input or output names
+            JarMappingLoadTransformer inputTransformer = null;
+            JarMappingLoadTransformer outputTransformer = null;
+
+            if (options.has("in-shade-relocation")) {
+                @SuppressWarnings("unchecked")
+                List<String> relocations = (List<String>) options.valuesOf("in-shade-relocation");
+
+                inputTransformer = new ShadeRelocationSimulator(relocations);
+            }
+
+            if (options.has("out-shade-relocation")) {
+                @SuppressWarnings("unchecked")
+                List<String> relocations = (List<String>) options.valuesOf("out-shade-relocation");
+
+                outputTransformer = new ShadeRelocationSimulator(relocations);
+            }
+
+            boolean reverse = options.has("reverse");
+
+            // Load each mapping
             @SuppressWarnings("unchecked")
-            List<String> specs = (List<String>) options.valuesOf("srg-in");
+            List<String> filenames = (List<String>) options.valuesOf("srg-in");
+            for (String filename : filenames) {
+                File file = new File(filename);
 
-            for (String spec : specs) {
-                if (options.has("shade-relocation")) {
-                    // legacy command-line option support
-                    // (new way is filename@... from the command-line, or loadMappings() programmatically)
-                    @SuppressWarnings("unchecked")
-                    List<String> relocations = (List<String>) options.valuesOf("shade-relocation");
-                    spec += "@" + Joiner.on(',').join(relocations);
+                if (file.isDirectory()) {
+                    jarMapping.loadMappingsDir(file, reverse);
+                } else {
+                    jarMapping.loadMappings(new BufferedReader(new FileReader(file)), inputTransformer, outputTransformer, reverse);
                 }
-
-                jarMapping.loadMappings(spec);
             }
         } else {
             System.err.println("No mappings given, first-jar/second-jar or srg-in required");