diff --git a/Cargo.lock b/Cargo.lock
index 63d9468..c517e53 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -183,7 +183,7 @@ checksum = "b94f61472cee1439c0b966b47e3aca9ae07e45d070759512cd390ea2bebc6675"
 
 [[package]]
 name = "codebase-to-prompt"
-version = "1.0.0"
+version = "1.0.1"
 dependencies = [
  "anyhow",
  "chrono",
diff --git a/Cargo.toml b/Cargo.toml
index b840d1d..1a23520 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -1,6 +1,6 @@
 [package]
 name = "codebase-to-prompt"
-version = "1.0.0"
+version = "1.0.1"
 edition = "2024"
 authors = ["Gabriel Kaszewski <gabrielkaszewski@gmail.com>"]
 license = "MIT"
diff --git a/src/lib.rs b/src/lib.rs
index c22a2cf..7eac05c 100644
--- a/src/lib.rs
+++ b/src/lib.rs
@@ -7,7 +7,7 @@ use chrono::Local;
 use clap::ValueEnum;
 use git2::Repository;
 use ignore::gitignore::Gitignore;
-use tracing::{error, info, warn};
+use tracing::{debug, error, info, warn};
 use walkdir::{DirEntry, WalkDir};
 
 /// Represents the output format for the bundled files.
@@ -26,8 +26,8 @@ pub enum Format {
 /// Configuration options for the file bundling process.
 #[derive(Debug)]
 pub struct Config {
-    /// The directory to process.
-    pub directory: PathBuf,
+    /// The directories to process.
+    pub directory: Vec<PathBuf>,
     /// The optional output file path. If not provided, output is written to stdout.
     pub output: Option<PathBuf>,
     /// File extensions to include in the output.
@@ -46,6 +46,8 @@ pub struct Config {
     pub ignore_hidden: bool,
     /// Whether to respect `.gitignore` rules.
     pub respect_gitignore: bool,
+    /// Whether to use relative paths in the output.
+    pub relative_path: bool,
 }
 
 /// Runs the file bundling process based on the provided configuration.
@@ -62,9 +64,20 @@ pub fn run(config: Config) -> Result<()> {
         append_date_and_git_hash(&mut output_path, &config)?;
     }
 
-    let writer = determine_output_writer(&output_path)?;
+    let mut writer = determine_output_writer(&output_path)?;
 
-    process_directory(&config, writer)
+    for dir in &config.directory {
+        if !dir.is_dir() {
+            return Err(anyhow::anyhow!(
+                "The specified path is not a directory: {}",
+                dir.display()
+            ));
+        }
+
+        process_directory(&config, &mut writer, dir)?;
+    }
+
+    Ok(())
 }
 
 /// Appends the current date and/or Git hash to the output file name if required.
@@ -90,16 +103,18 @@ fn append_date_and_git_hash(output_path: &mut Option<PathBuf>, config: &Config)
         }
 
         if config.append_git_hash {
-            match Repository::open(&config.directory) {
-                Ok(repo) => {
-                    let head = repo.head().context("Failed to get repository HEAD")?;
-                    if let Some(oid) = head.target() {
-                        new_filename.push('_');
-                        new_filename.push_str(&oid.to_string()[..7]);
-                        info!("Appending git hash to filename.");
+            for dir in &config.directory {
+                match Repository::open(&dir) {
+                    Ok(repo) => {
+                        let head = repo.head().context("Failed to get repository HEAD")?;
+                        if let Some(oid) = head.target() {
+                            new_filename.push('_');
+                            new_filename.push_str(&oid.to_string()[..7]);
+                            info!("Appending git hash to filename.");
+                        }
                     }
+                    Err(_) => warn!("Not a git repository, cannot append git hash."),
                 }
-                Err(_) => warn!("Not a git repository, cannot append git hash."),
             }
         }
 
@@ -139,23 +154,26 @@ fn determine_output_writer(output_path: &Option<PathBuf>) -> Result<Box<dyn Writ
 ///
 /// # Returns
 /// * `Result<()>` - Returns `Ok(())` if successful, or an error if the process fails.
-fn process_directory(config: &Config, mut writer: Box<dyn Write>) -> Result<()> {
-    let (gitignore, _) = Gitignore::new(config.directory.join(".gitignore"));
+fn process_directory(config: &Config, writer: &mut dyn Write, dir: &PathBuf) -> Result<()> {
+    let (gitignore, _) = Gitignore::new(dir.join(".gitignore"));
 
-    let walker = WalkDir::new(&config.directory)
+    let walker = WalkDir::new(dir)
         .into_iter()
         .filter_entry(|e| should_include_entry(e, &gitignore, config));
 
     for result in walker {
         let entry = match result {
-            Ok(entry) => entry,
+            Ok(entry) => {
+                debug!("Processing entry: {:?}", entry);
+                entry
+            }
             Err(err) => {
                 error!("Failed to access entry: {}", err);
                 continue;
             }
         };
 
-        if let Err(err) = process_file_entry(&entry, &mut writer, config) {
+        if let Err(err) = process_file_entry(&entry, writer, config, dir) {
             error!("{}", err);
         }
     }
@@ -186,26 +204,37 @@ fn should_include_entry(entry: &DirEntry, gitignore: &Gitignore, config: &Config
 ///
 /// # Returns
 /// * `Result<()>` - Returns `Ok(())` if successful, or an error if the process fails.
-fn process_file_entry(entry: &DirEntry, writer: &mut dyn Write, config: &Config) -> Result<()> {
+fn process_file_entry(
+    entry: &DirEntry,
+    writer: &mut dyn Write,
+    config: &Config,
+    dir: &PathBuf,
+) -> Result<()> {
+    debug!("File process entry process for {:?}", entry.path());
+
     let path = entry.path();
     if !path.is_file() {
+        debug!("{:?} is not a file.", path);
         return Ok(());
     }
 
     let extension = path.extension().and_then(|s| s.to_str()).unwrap_or("");
 
-    let apply_include_filter =
-        !(config.include.is_empty() || config.include.len() == 1 && config.include[0].is_empty());
+    debug!("Extension {:?} for {:?}", extension, path);
+
+    let apply_include_filter = !(config.include.is_empty());
 
     if apply_include_filter && !config.include.contains(&extension.to_string()) {
         return Ok(());
     }
 
-    if config.exclude.contains(&extension.to_string()) {
+    let apply_exclude_filter = !(config.exclude.is_empty());
+
+    if apply_exclude_filter && config.exclude.contains(&extension.to_string()) {
         return Ok(());
     }
 
-    let relative_path = path.strip_prefix(&config.directory).unwrap_or(path);
+    let relative_path = path.strip_prefix(dir).unwrap_or(path);
     let content = match fs::read_to_string(path) {
         Ok(content) => content,
         Err(_) => {
@@ -214,8 +243,17 @@ fn process_file_entry(entry: &DirEntry, writer: &mut dyn Write, config: &Config)
         }
     };
 
-    write_file_content(writer, relative_path, &content, extension, config)
-        .with_context(|| format!("Failed to write file content for {}", path.display()))
+    match &config.relative_path {
+        true => write_file_content(writer, relative_path, &content, extension, config)
+            .with_context(|| {
+                format!(
+                    "Failed to write file content for {}",
+                    relative_path.display()
+                )
+            }),
+        false => write_file_content(writer, path, &content, extension, config)
+            .with_context(|| format!("Failed to write file content for {}", path.display())),
+    }
 }
 
 /// Writes the content of a single file to the writer based on the specified format.
diff --git a/src/main.rs b/src/main.rs
index 2d02931..ea43a1e 100644
--- a/src/main.rs
+++ b/src/main.rs
@@ -8,16 +8,16 @@ use tracing_subscriber::FmtSubscriber;
 #[derive(Parser, Debug)]
 #[command(author, version, about, long_about = None)]
 struct Args {
-    #[arg(default_value = ".")]
-    directory: PathBuf,
+    #[arg(default_value = ".", value_delimiter = ' ', num_args=1..)]
+    directory: Vec<PathBuf>,
 
     #[arg(short, long)]
     output: Option<PathBuf>,
 
-    #[arg(short, long, use_value_delimiter = true, default_value = "")]
+    #[arg(short, long, value_delimiter = ',', num_args = 0..)]
     include: Vec<String>,
 
-    #[arg(short, long, use_value_delimiter = true, default_value = "")]
+    #[arg(short, long, value_delimiter = ',', num_args = 0..)]
     exclude: Vec<String>,
 
     #[arg(long, value_enum, default_value_t = Format::Console)]
@@ -32,16 +32,19 @@ struct Args {
     #[arg(short = 'l', long)]
     line_numbers: bool,
 
-    #[arg(short = 'H', long)]
+    #[arg(short = 'H', long, default_value_t = true)]
     ignore_hidden: bool,
 
     #[arg(short = 'R', long, default_value_t = true)]
     respect_gitignore: bool,
+
+    #[arg(long, default_value_t = false)]
+    relative_path: bool,
 }
 
 fn main() -> Result<()> {
     let subscriber = FmtSubscriber::builder()
-        .with_max_level(LevelFilter::INFO)
+        .with_max_level(LevelFilter::DEBUG)
         .finish();
     tracing::subscriber::set_global_default(subscriber).expect("setting default subscriber failed");
 
@@ -69,6 +72,7 @@ fn main() -> Result<()> {
         line_numbers: args.line_numbers,
         ignore_hidden: args.ignore_hidden,
         respect_gitignore: args.respect_gitignore,
+        relative_path: args.relative_path,
     };
 
     debug!("Starting codebase to prompt with config: {:?}", config);
diff --git a/tests/integration_tests.rs b/tests/integration_tests.rs
index 89859c4..fc90fb8 100644
--- a/tests/integration_tests.rs
+++ b/tests/integration_tests.rs
@@ -8,7 +8,7 @@ fn test_run_with_markdown_format() {
     let output_file = temp_dir.path().join("output.md");
 
     let config = Config {
-        directory: PathBuf::from("tests/fixtures"),
+        directory: vec![PathBuf::from("tests/fixtures")],
         output: Some(output_file.clone()),
         include: vec!["rs".to_string()],
         exclude: vec![],
@@ -18,6 +18,7 @@ fn test_run_with_markdown_format() {
         line_numbers: false,
         ignore_hidden: true,
         respect_gitignore: true,
+        relative_path: false,
     };
 
     let result = run(config);
@@ -33,7 +34,7 @@ fn test_run_with_text_format() {
     let output_file = temp_dir.path().join("output.txt");
 
     let config = Config {
-        directory: PathBuf::from("tests/fixtures"),
+        directory: vec![PathBuf::from("tests/fixtures")],
         output: Some(output_file.clone()),
         include: vec!["txt".to_string()],
         exclude: vec![],
@@ -43,6 +44,7 @@ fn test_run_with_text_format() {
         line_numbers: true,
         ignore_hidden: true,
         respect_gitignore: true,
+        relative_path: false,
     };
 
     let result = run(config);
@@ -58,7 +60,7 @@ fn test_run_with_git_hash_append() {
     let output_file = temp_dir.path().join("output.txt");
 
     let config = Config {
-        directory: PathBuf::from("tests/fixtures"),
+        directory: vec![PathBuf::from("tests/fixtures")],
         output: Some(output_file.clone()),
         include: vec!["txt".to_string()],
         exclude: vec![],
@@ -68,6 +70,7 @@ fn test_run_with_git_hash_append() {
         line_numbers: false,
         ignore_hidden: true,
         respect_gitignore: true,
+        relative_path: false,
     };
 
     let result = run(config);