diff --git a/src/main/java/org/cobbzilla/util/main/FileHeader.java b/src/main/java/org/cobbzilla/util/main/FileHeader.java
index c2452d6..56df732 100644
--- a/src/main/java/org/cobbzilla/util/main/FileHeader.java
+++ b/src/main/java/org/cobbzilla/util/main/FileHeader.java
@@ -10,10 +10,10 @@ public class FileHeader {
     @Getter @Setter private String ext;
     @Getter @Setter private String header;
     @Getter @Setter private String regex;
-    @Getter(lazy=true) private final Pattern pattern = Pattern.compile(getRegex()+"\n", Pattern.MULTILINE);
+    @Getter(lazy=true) private final Pattern pattern = Pattern.compile(getRegex()+"\n", Pattern.MULTILINE | Pattern.DOTALL);
 
     @Getter @Setter private String prefix;
     public boolean hasPrefix () { return prefix != null; }
-    @Getter(lazy=true) private final Pattern prefixPattern = Pattern.compile(getPrefix()+"\n", Pattern.MULTILINE);
+    @Getter(lazy=true) private final Pattern prefixPattern = Pattern.compile(getPrefix()+"\n", Pattern.MULTILINE | Pattern.DOTALL);
 
 }
diff --git a/src/main/java/org/cobbzilla/util/main/FileHeaderMain.java b/src/main/java/org/cobbzilla/util/main/FileHeaderMain.java
index 1fa482d..d826dfa 100644
--- a/src/main/java/org/cobbzilla/util/main/FileHeaderMain.java
+++ b/src/main/java/org/cobbzilla/util/main/FileHeaderMain.java
@@ -18,6 +18,10 @@ public class FileHeaderMain extends BaseMain<FileHeaderOptions> {
         new FilesystemWalker()
                 .withDir(opts.getDir())
                 .withVisitor(file -> {
+                    if (opts.exclude(file)) {
+                        err("excluding: "+abs(file));
+                        return;
+                    }
                     final String ext = FileUtil.extension(file);
                     final FileHeader header = headers.get(ext.length() > 0 ? ext.substring(1) : ext);
                     if (header != null) {
diff --git a/src/main/java/org/cobbzilla/util/main/FileHeaderOptions.java b/src/main/java/org/cobbzilla/util/main/FileHeaderOptions.java
index 55d3288..c552652 100644
--- a/src/main/java/org/cobbzilla/util/main/FileHeaderOptions.java
+++ b/src/main/java/org/cobbzilla/util/main/FileHeaderOptions.java
@@ -9,10 +9,14 @@ import java.io.File;
 import java.io.IOException;
 import java.io.InputStream;
 import java.util.Arrays;
+import java.util.Collections;
+import java.util.List;
 import java.util.Map;
 import java.util.stream.Collectors;
 
 import static java.util.function.Function.identity;
+import static org.cobbzilla.util.daemon.ZillaRuntime.empty;
+import static org.cobbzilla.util.io.FileUtil.abs;
 import static org.cobbzilla.util.json.JsonUtil.FULL_MAPPER_ALLOW_COMMENTS;
 import static org.cobbzilla.util.json.JsonUtil.json;
 import static org.cobbzilla.util.string.StringUtil.UTF8cs;
@@ -42,4 +46,20 @@ public class FileHeaderOptions extends BaseMainOptions {
         return Arrays.stream(headers).collect(Collectors.toMap(FileHeader::getExt, identity()));
     }
 
+    public static final String USAGE_EXCLUDE_PATHS = "Paths (or path parts) to exclude, separated by commas";
+    public static final String OPT_EXCLUDE_PATHS = "-e";
+    public static final String LONGOPT_EXCLUDE_PATHS = "--exclude-paths";
+    @Option(name=OPT_EXCLUDE_PATHS, aliases=LONGOPT_EXCLUDE_PATHS, usage=USAGE_EXCLUDE_PATHS)
+    @Getter @Setter private String excludePaths;
+
+    @Getter(lazy=true) private final List<String> excludePathPatterns = initExcludePatterns();
+
+    private List<String> initExcludePatterns() {
+        if (empty(excludePaths)) return Collections.emptyList();
+        final String[] parts = excludePaths.split(",");
+        return Arrays.stream(parts).collect(Collectors.toList());
+    }
+
+    public boolean exclude(File f) { return getExcludePathPatterns().stream().anyMatch(p -> abs(f).contains(p)); }
+
 }