Add bundles, relinking and repair of updated entries

- bundle: move a binary and its companion files into their own folder,
  picking the main executable with --main, zenity or kdialog
- relink: point an entry at a different executable
- repair: follow AppImages that were renamed or replaced by an update,
  matched by update info, embedded desktop id or version-stripped name

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

packaging/arch/PKGBUILD

@@ -11,6 +11,7 @@ optdepends=(
   'thunar: context menu integration'
   'desktop-file-utils: refresh the menu cache after changes'
   'libnotify: notifications from context menu actions'
+  'zenity: choose the main binary when a bundle has several executables'
 )
 options=('!lto')
 

src/appimage.rs

@@ -2,7 +2,7 @@ use std::{
     collections::HashMap,
     ffi::OsStr,
     fs::File,
-    io::{BufReader, Read},
+    io::{BufReader, Read, Seek, SeekFrom},
     path::{Component, Path, PathBuf},
 };
 
@@ -22,13 +22,7 @@ pub struct Embedded {
 }
 
 pub fn read(path: &Path, offset: u64) -> Result<Embedded> {
-    let file = BufReader::new(File::open(path)?);
+    let fs = open(path, offset)?;
-    let fs = FilesystemReader::from_reader_with_offset(file, offset).with_context(|| {
-        format!(
-            "cannot read the squashfs image embedded in {}",
-            path.display()
-        )
-    })?;
     let image = Image::new(&fs);
     let desktop = image.root_desktop();
     let icon_name = desktop.as_ref().and_then(|d| d.get("Icon"));
@@ -36,6 +30,100 @@ pub fn read(path: &Path, offset: u64) -> Result<Embedded> {
     Ok(Embedded { desktop, icon })
 }
 
+pub fn desktop_id(path: &Path, offset: u64) -> Option<String> {
+    let fs = open(path, offset).ok()?;
+    let image = Image::new(&fs);
+    let name = image.root_desktop_path()?.file_name()?;
+    Some(name.to_string_lossy().into_owned())
+}
+
+pub fn update_info(path: &Path) -> Option<String> {
+    let mut file = File::open(path).ok()?;
+    let mut header = [0u8; 64];
+    file.read_exact(&mut header).ok()?;
+    if !header.starts_with(b"\x7fELF") {
+        return None;
+    }
+    let little_endian = header[5] == 1;
+    let wide = match header[4] {
+        1 => false,
+        2 => true,
+        _ => return None,
+    };
+    let uint = |bytes: &[u8], offset: usize, len: usize| -> Option<u64> {
+        let bytes = bytes.get(offset..offset + len)?;
+        let fold = |acc: u64, &b: &u8| (acc << 8) | u64::from(b);
+        Some(if little_endian {
+            bytes.iter().rev().fold(0, fold)
+        } else {
+            bytes.iter().fold(0, fold)
+        })
+    };
+    let (shoff, shentsize, shnum, shstrndx) = if wide {
+        (
+            uint(&header, 0x28, 8)?,
+            uint(&header, 0x3A, 2)?,
+            uint(&header, 0x3C, 2)?,
+            uint(&header, 0x3E, 2)?,
+        )
+    } else {
+        (
+            uint(&header, 0x20, 4)?,
+            uint(&header, 0x2E, 2)?,
+            uint(&header, 0x30, 2)?,
+            uint(&header, 0x32, 2)?,
+        )
+    };
+    let mut table = vec![0u8; usize::try_from(shentsize * shnum).ok()?];
+    file.seek(SeekFrom::Start(shoff)).ok()?;
+    file.read_exact(&mut table).ok()?;
+    let section = |index: u64| -> Option<(u64, u64, u64)> {
+        let base = usize::try_from(index * shentsize).ok()?;
+        let name = uint(&table, base, 4)?;
+        Some(if wide {
+            (
+                name,
+                uint(&table, base + 0x18, 8)?,
+                uint(&table, base + 0x20, 8)?,
+            )
+        } else {
+            (
+                name,
+                uint(&table, base + 0x10, 4)?,
+                uint(&table, base + 0x14, 4)?,
+            )
+        })
+    };
+    let mut read_at = |offset: u64, size: u64| -> Option<Vec<u8>> {
+        let mut data = vec![0u8; usize::try_from(size.min(1 << 16)).ok()?];
+        file.seek(SeekFrom::Start(offset)).ok()?;
+        file.read_exact(&mut data).ok()?;
+        Some(data)
+    };
+    let (_, names_offset, names_size) = section(shstrndx)?;
+    let names = read_at(names_offset, names_size)?;
+    let (_, offset, size) = (0..shnum).filter_map(section).find(|(name, _, _)| {
+        usize::try_from(*name)
+            .ok()
+            .and_then(|start| names.get(start..))
+            .is_some_and(|rest| rest.starts_with(b".upd_info\0"))
+    })?;
+    let data = read_at(offset, size)?;
+    let end = data.iter().position(|&b| b == 0).unwrap_or(data.len());
+    let info = String::from_utf8_lossy(&data[..end]).trim().to_string();
+    (!info.is_empty()).then_some(info)
+}
+
+fn open(path: &Path, offset: u64) -> Result<FilesystemReader<'static>> {
+    let file = BufReader::new(File::open(path)?);
+    FilesystemReader::from_reader_with_offset(file, offset).with_context(|| {
+        format!(
+            "cannot read the squashfs image embedded in {}",
+            path.display()
+        )
+    })
+}
+
 struct Image<'a, 'b> {
     fs: &'a FilesystemReader<'b>,
     nodes: HashMap<PathBuf, &'a InnerNode<SquashfsFileReader>>,
@@ -69,14 +157,15 @@ impl<'a, 'b> Image<'a, 'b> {
         None
     }
 
-    fn root_desktop(&self) -> Option<DesktopEntry> {
+    fn root_desktop_path(&self) -> Option<&PathBuf> {
-        let mut candidates: Vec<&PathBuf> = self
+        self.nodes
-            .nodes
             .keys()
             .filter(|p| p.components().count() == 1 && p.extension() == Some(OsStr::new("desktop")))
-            .collect();
+            .min()
-        candidates.sort();
+    }
-        let data = self.read(candidates.first()?)?;
+
+    fn root_desktop(&self) -> Option<DesktopEntry> {
+        let data = self.read(self.root_desktop_path()?)?;
         Some(DesktopEntry::parse(&String::from_utf8_lossy(&data)))
     }
 

src/identity.rs

@@ -0,0 +1,67 @@
+use std::path::Path;
+
+use crate::{
+    appimage,
+    detect::{self, Kind},
+};
+
+const UPDATE: &str = "update:";
+const DESKTOP: &str = "desktop:";
+const NAME: &str = "name:";
+
+const ARCH_TOKENS: [&str; 8] = [
+    "x86", "amd64", "aarch64", "arm64", "armhf", "i386", "i686", "linux",
+];
+
+pub fn identify(path: &Path) -> String {
+    update(path)
+        .or_else(|| desktop(path))
+        .unwrap_or_else(|| name(path))
+}
+
+pub fn matches(identity: &str, path: &Path) -> bool {
+    let actual = if identity.starts_with(UPDATE) {
+        update(path)
+    } else if identity.starts_with(DESKTOP) {
+        desktop(path)
+    } else {
+        Some(name(path))
+    };
+    actual.as_deref() == Some(identity)
+}
+
+pub fn is_strong(identity: &str) -> bool {
+    !identity.starts_with(NAME)
+}
+
+pub fn name(path: &Path) -> String {
+    let stem = path
+        .file_stem()
+        .map(|s| s.to_string_lossy().to_lowercase())
+        .unwrap_or_default();
+    let base = stem
+        .split(['-', '_', '.', ' '])
+        .filter(|token| {
+            let versioned = token.starts_with(|c: char| c.is_ascii_digit())
+                || token
+                    .strip_prefix('v')
+                    .is_some_and(|rest| rest.starts_with(|c: char| c.is_ascii_digit()));
+            !token.is_empty() && !versioned && !ARCH_TOKENS.contains(token)
+        })
+        .collect::<Vec<_>>()
+        .join("-");
+    format!("{NAME}{}", if base.is_empty() { stem } else { base })
+}
+
+fn update(path: &Path) -> Option<String> {
+    appimage::update_info(path).map(|info| format!("{UPDATE}{info}"))
+}
+
+fn desktop(path: &Path) -> Option<String> {
+    match detect::detect(path).ok()? {
+        Kind::AppImage(Some(offset)) => {
+            appimage::desktop_id(path, offset).map(|id| format!("{DESKTOP}{id}"))
+        }
+        _ => None,
+    }
+}

src/main.rs

@@ -3,6 +3,8 @@ mod config;
 mod desktop;
 mod detect;
 mod fastfetch;
+mod identity;
+mod picker;
 mod store;
 mod thunar;
 mod tui;
@@ -37,6 +39,16 @@ enum Command {
         #[arg(required = true)]
         files: Vec<PathBuf>,
     },
+    /// Move a binary and its companion files into their own folder and create a menu entry
+    Bundle {
+        #[arg(long)]
+        notify: bool,
+        /// The file that starts the application, detected when omitted
+        #[arg(long)]
+        main: Option<PathBuf>,
+        #[arg(required = true)]
+        files: Vec<PathBuf>,
+    },
     /// Remove the menu entries of integrated files
     Remove {
         #[arg(long)]
@@ -47,6 +59,15 @@ enum Command {
         #[arg(required = true)]
         files: Vec<PathBuf>,
     },
+    /// Point an entry at a different executable, e.g. after an AppImage renamed itself
+    Relink {
+        /// The entry's id (ratbin-…), name, or current file
+        entry: String,
+        /// The executable the entry should start
+        file: PathBuf,
+    },
+    /// Point entries whose file was renamed or replaced by an update at the new file
+    Repair,
     /// List integrated files
     List,
     /// Open the interactive manager (default)
@@ -84,6 +105,16 @@ fn run(cli: Cli) -> Result<ExitCode> {
             let apps_dir = Config::load()?.apps_dir()?;
             store::integrate(&apps_dir, file).map(|i| i.name())
         })),
+        Command::Bundle {
+            notify,
+            main,
+            files,
+        } => {
+            let result = Config::load()?.apps_dir().and_then(|apps_dir| {
+                store::integrate_bundle(&apps_dir, &files, main.as_deref(), picker::choose_main)
+            });
+            Ok(report("Integrated", notify, vec![result.map(|i| i.name())]))
+        }
         Command::Remove {
             notify,
             delete,
@@ -91,6 +122,23 @@ fn run(cli: Cli) -> Result<ExitCode> {
         } => Ok(batch("Removed", notify, &files, |file| {
             store::remove_path(file, delete)
         })),
+        Command::Relink { entry, file } => {
+            let mut integration = store::find_entry(&entry)?;
+            store::relink(&mut integration, &file)?;
+            println!(
+                "Relinked: {} → {}",
+                integration.name(),
+                integration.source().display()
+            );
+            Ok(ExitCode::SUCCESS)
+        }
+        Command::Repair => {
+            let results = store::repair()?;
+            if results.is_empty() {
+                println!("Nothing to repair");
+            }
+            Ok(report("Repaired", false, results))
+        }
         Command::List => {
             for integration in store::list()? {
                 println!(
@@ -133,10 +181,14 @@ fn batch(
     files: &[PathBuf],
     op: impl Fn(&Path) -> Result<String>,
 ) -> ExitCode {
+    report(verb, notify, files.iter().map(|file| op(file)).collect())
+}
+
+fn report(verb: &str, notify: bool, results: Vec<Result<String>>) -> ExitCode {
     let mut done = Vec::new();
     let mut failed = Vec::new();
-    for file in files {
+    for result in results {
-        match op(file) {
+        match result {
             Ok(name) => {
                 println!("{verb}: {name}");
                 done.push(name);

src/picker.rs

@@ -0,0 +1,67 @@
+use std::{
+    io,
+    path::PathBuf,
+    process::{Command, Output},
+};
+
+use anyhow::{Context, Result, bail};
+
+const PROMPT: &str = "Which file starts the application?";
+
+pub fn choose_main(candidates: &[PathBuf]) -> Result<PathBuf> {
+    let names: Vec<String> = candidates
+        .iter()
+        .map(|path| {
+            path.file_name()
+                .map(|n| n.to_string_lossy().into_owned())
+                .unwrap_or_default()
+        })
+        .collect();
+    let output = match zenity(&names) {
+        Err(e) if e.kind() == io::ErrorKind::NotFound => kdialog(&names),
+        other => other,
+    };
+    let output = match output {
+        Ok(output) => output,
+        Err(e) if e.kind() == io::ErrorKind::NotFound => bail!(
+            "several executables selected ({}); choose one with --main",
+            names.join(", ")
+        ),
+        Err(e) => return Err(e).context("cannot show the selection dialog"),
+    };
+    if !output.status.success() {
+        bail!("no main executable chosen");
+    }
+    String::from_utf8_lossy(&output.stdout)
+        .trim()
+        .parse::<usize>()
+        .ok()
+        .and_then(|index| candidates.get(index).cloned())
+        .context("the selection dialog returned an unknown choice")
+}
+
+fn zenity(names: &[String]) -> io::Result<Output> {
+    let mut command = Command::new("zenity");
+    command.args([
+        "--list",
+        "--title=ratbin",
+        &format!("--text={PROMPT}"),
+        "--column=#",
+        "--column=File",
+        "--hide-column=1",
+        "--print-column=1",
+    ]);
+    for (index, name) in names.iter().enumerate() {
+        command.arg(index.to_string()).arg(name);
+    }
+    command.output()
+}
+
+fn kdialog(names: &[String]) -> io::Result<Output> {
+    let mut command = Command::new("kdialog");
+    command.args(["--title", "ratbin", "--menu", PROMPT]);
+    for (index, name) in names.iter().enumerate() {
+        command.arg(index.to_string()).arg(name);
+    }
+    command.output()
+}

src/store.rs

@@ -1,21 +1,27 @@
 use std::{
+    collections::HashSet,
+    ffi::OsStr,
     fs, io,
-    os::unix::fs::PermissionsExt,
+    os::unix::fs::{PermissionsExt, symlink},
     path::{Path, PathBuf},
     process::{Command, Stdio},
+    time::SystemTime,
 };
 
-use anyhow::{Context, Result, bail};
+use anyhow::{Context, Result, anyhow, bail};
 
 use crate::{
     appimage, config,
     desktop::{self, DesktopEntry},
     detect::{self, Kind},
+    identity,
 };
 
 const KEY_SOURCE: &str = "X-Ratbin-Source";
 const KEY_ARGS: &str = "X-Ratbin-Args";
 const KEY_KIND: &str = "X-Ratbin-Kind";
+const KEY_BUNDLE: &str = "X-Ratbin-Bundle";
+const KEY_IDENTITY: &str = "X-Ratbin-Identity";
 const PREFIX: &str = "ratbin-";
 
 pub struct Integration {
@@ -50,6 +56,10 @@ impl Integration {
         self.entry.get(KEY_KIND).unwrap_or_default()
     }
 
+    pub fn bundle(&self) -> Option<PathBuf> {
+        self.entry.get(KEY_BUNDLE).map(PathBuf::from)
+    }
+
     pub fn fields(&self) -> Fields {
         let get = |key: &str| self.entry.get(key).unwrap_or_default();
         Fields {
@@ -119,18 +129,75 @@ pub fn list() -> Result<Vec<Integration>> {
     Ok(out)
 }
 
-fn find(source: &Path) -> Result<Option<Integration>> {
+fn find(path: &Path) -> Result<Option<Integration>> {
-    Ok(list()?.into_iter().find(|i| i.source() == source))
+    Ok(list()?
+        .into_iter()
+        .find(|i| i.source() == path || i.bundle().as_deref() == Some(path)))
 }
 
-pub fn integrate(apps_dir: &Path, path: &Path) -> Result<Integration> {
+pub fn find_entry(query: &str) -> Result<Integration> {
-    let src = path
+    let path = fs::canonicalize(query).or_else(|_| std::path::absolute(query))?;
-        .canonicalize()
+    let mut matches: Vec<Integration> = list()?
-        .with_context(|| format!("cannot access {}", path.display()))?;
+        .into_iter()
+        .filter(|i| {
+            i.source() == path
+                || i.bundle().as_deref() == Some(path.as_path())
+                || i.desktop_path.file_stem() == Some(OsStr::new(query))
+                || i.name().eq_ignore_ascii_case(query)
+        })
+        .collect();
+    match matches.len() {
+        0 => bail!("no integrated entry matches \"{query}\""),
+        1 => Ok(matches.remove(0)),
+        _ => bail!(
+            "\"{query}\" matches several entries ({}); use the entry id instead",
+            matches
+                .iter()
+                .map(|i| file_stem(&i.desktop_path))
+                .collect::<Vec<_>>()
+                .join(", ")
+        ),
+    }
+}
+
+pub fn relink_candidates(integration: &Integration) -> Result<Vec<PathBuf>> {
+    let source = integration.source();
+    let dir = match integration
+        .bundle()
+        .or_else(|| source.parent().map(Path::to_path_buf))
+    {
+        Some(dir) if dir.is_dir() => dir,
+        _ => config::Config::load()?.apps_dir()?,
+    };
+    let taken: HashSet<PathBuf> = list()?
+        .iter()
+        .filter(|i| i.desktop_path != integration.desktop_path)
+        .map(Integration::source)
+        .collect();
+    let Ok(entries) = fs::read_dir(&dir) else {
+        return Ok(Vec::new());
+    };
+    let mut files: Vec<(PathBuf, SystemTime)> = entries
+        .flatten()
+        .map(|e| e.path())
+        .filter(|path| !taken.contains(path) && is_candidate(path))
+        .map(|path| {
+            let modified = modified(&path);
+            (path, modified)
+        })
+        .collect();
+    files.sort_by_key(|(_, modified)| std::cmp::Reverse(*modified));
+    Ok(files.into_iter().map(|(path, _)| path).collect())
+}
+
+pub fn relink(integration: &mut Integration, path: &Path) -> Result<()> {
+    let src = canonical(path)?;
     if !src.is_file() {
         bail!("{} is not a file", src.display());
     }
-    if let Some(existing) = find(&src)? {
+    if let Some(existing) = find(&src)?
+        && existing.desktop_path != integration.desktop_path
+    {
         bail!(
             "{} is already integrated as \"{}\"",
             src.display(),
@@ -138,10 +205,185 @@ pub fn integrate(apps_dir: &Path, path: &Path) -> Result<Integration> {
         );
     }
     let kind = detect::detect(&src)?;
-    let target = place(apps_dir, &src)?;
+    make_executable(&src)?;
-    make_executable(&target)?;
+
-    let id = unique_id(&target)?;
+    let bundle = integration.bundle();
-    let entry = build_entry(&kind, &target, &id)?;
+    let entry = &mut integration.entry;
+    let fallbacks = [Kind::Elf, Kind::Script].map(|k| k.fallback_icon());
+    if entry
+        .get("Icon")
+        .is_some_and(|icon| fallbacks.contains(&icon.as_str()))
+    {
+        entry.set("Icon", kind.fallback_icon());
+    }
+    if bundle.is_some_and(|bundle| src.parent() != Some(bundle.as_path())) {
+        entry.remove(KEY_BUNDLE);
+        entry.remove("Path");
+    }
+    entry.map_values("Exec", |exec| {
+        desktop::build_exec(&src, desktop::exec_args(exec))
+    });
+    let args = entry.get(KEY_ARGS).unwrap_or_default();
+    entry.set("Exec", &desktop::build_exec(&src, &args));
+    entry.set(KEY_SOURCE, &src.to_string_lossy());
+    entry.set(KEY_KIND, kind.label());
+    entry.set(KEY_IDENTITY, &identity::identify(&src));
+    save(integration)
+}
+
+pub fn repair() -> Result<Vec<Result<String>>> {
+    Ok(list()?
+        .into_iter()
+        .filter_map(|mut integration| repair_one(&mut integration).transpose())
+        .collect())
+}
+
+fn repair_one(integration: &mut Integration) -> Result<Option<String>> {
+    let source = integration.source();
+    let present = source.is_file();
+    let identity = match integration.entry.get(KEY_IDENTITY) {
+        Some(identity) => identity,
+        None if present => {
+            let identity = identity::identify(&source);
+            integration.entry.set(KEY_IDENTITY, &identity);
+            save(integration)?;
+            identity
+        }
+        None => identity::name(&source),
+    };
+    // Weak name-based identities only fix missing files, never replace a working one.
+    if present && !identity::is_strong(&identity) {
+        return Ok(None);
+    }
+    let current = modified(&source);
+    let replacement = relink_candidates(integration)?
+        .into_iter()
+        .take_while(|path| !present || modified(path) > current)
+        .find(|path| identity::matches(&identity, path));
+    let Some(replacement) = replacement else {
+        if present {
+            return Ok(None);
+        }
+        return Err(anyhow!(
+            "{}: {} is missing and no replacement was found",
+            integration.name(),
+            source.display()
+        ));
+    };
+    relink(integration, &replacement)?;
+    Ok(Some(format!(
+        "{} → {}",
+        integration.name(),
+        replacement
+            .file_name()
+            .unwrap_or_default()
+            .to_string_lossy()
+    )))
+}
+
+pub fn integrate(apps_dir: &Path, path: &Path) -> Result<Integration> {
+    let src = canonical(path)?;
+    let kind = check_main(&src)?;
+    let apps_dir = prepare_apps_dir(apps_dir)?;
+    let target = if src.starts_with(&apps_dir) {
+        src
+    } else {
+        let dest = apps_dir.join(file_name(&src)?);
+        move_to(&src, &dest)?;
+        dest
+    };
+    create(&kind, &target, None)
+}
+
+pub fn integrate_bundle(
+    apps_dir: &Path,
+    paths: &[PathBuf],
+    main: Option<&Path>,
+    choose: impl FnOnce(&[PathBuf]) -> Result<PathBuf>,
+) -> Result<Integration> {
+    let mut srcs = Vec::new();
+    for path in paths.iter().map(PathBuf::as_path).chain(main) {
+        let src = canonical(path)?;
+        if !srcs.contains(&src) {
+            srcs.push(src);
+        }
+    }
+    let main = match main {
+        Some(main) => canonical(main)?,
+        None => {
+            let mut candidates: Vec<PathBuf> = srcs
+                .iter()
+                .filter(|src| is_candidate(src))
+                .cloned()
+                .collect();
+            match candidates.len() {
+                0 => bail!("the selection contains no AppImage, ELF binary or script"),
+                1 => candidates.remove(0),
+                _ => choose(&candidates)?,
+            }
+        }
+    };
+    let kind = check_main(&main)?;
+    let apps_dir = prepare_apps_dir(apps_dir)?;
+    let bundle = apps_dir.join(file_stem(&main));
+    let in_place = srcs
+        .iter()
+        .all(|src| src.parent() == Some(bundle.as_path()));
+    if !in_place {
+        if bundle.exists() {
+            bail!("{} already exists", bundle.display());
+        }
+        let mut names = HashSet::new();
+        for src in &srcs {
+            let name = file_name(src)?;
+            if !names.insert(name) {
+                bail!(
+                    "more than one selected item is named {}",
+                    name.to_string_lossy()
+                );
+            }
+        }
+        fs::create_dir(&bundle).with_context(|| format!("cannot create {}", bundle.display()))?;
+        for src in &srcs {
+            move_to(src, &bundle.join(file_name(src)?))?;
+        }
+    }
+    let target = bundle.join(file_name(&main)?);
+    create(&kind, &target, Some(&bundle))
+}
+
+fn check_main(src: &Path) -> Result<Kind> {
+    if !src.is_file() {
+        bail!("{} is not a file", src.display());
+    }
+    if let Some(existing) = find(src)? {
+        bail!(
+            "{} is already integrated as \"{}\"",
+            src.display(),
+            existing.name()
+        );
+    }
+    detect::detect(src)
+}
+
+fn is_candidate(path: &Path) -> bool {
+    let name = path
+        .file_name()
+        .map(|n| n.to_string_lossy())
+        .unwrap_or_default();
+    let shared_lib = name.ends_with(".so") || name.contains(".so.");
+    path.is_file() && !shared_lib && detect::detect(path).is_ok()
+}
+
+fn create(kind: &Kind, target: &Path, bundle: Option<&Path>) -> Result<Integration> {
+    make_executable(target)?;
+    let id = unique_id(target)?;
+    let mut entry = build_entry(kind, target, &id)?;
+    if let Some(bundle) = bundle {
+        let bundle = bundle.to_string_lossy();
+        entry.set("Path", &bundle);
+        entry.set(KEY_BUNDLE, &bundle);
+    }
     let integration = Integration {
         desktop_path: config::applications_dir()?.join(format!("{id}.desktop")),
         entry,
@@ -151,9 +393,7 @@ pub fn integrate(apps_dir: &Path, path: &Path) -> Result<Integration> {
 }
 
 pub fn remove_path(path: &Path, delete_file: bool) -> Result<String> {
-    let src = path
+    let src = canonical(path)?;
-        .canonicalize()
-        .with_context(|| format!("cannot access {}", path.display()))?;
     let integration =
         find(&src)?.with_context(|| format!("{} is not integrated", src.display()))?;
     remove(&integration, delete_file)?;
@@ -168,7 +408,23 @@ pub fn remove(integration: &Integration, delete_file: bool) -> Result<()> {
         remove_if_exists(&icon)?;
     }
     if delete_file {
-        remove_if_exists(&integration.source())?;
+        let source = integration.source();
+        match integration.bundle() {
+            Some(bundle) if source.parent() == Some(bundle.as_path()) => {
+                match fs::remove_dir_all(&bundle) {
+                    Err(e) if e.kind() != io::ErrorKind::NotFound => {
+                        Err(e).with_context(|| format!("cannot remove {}", bundle.display()))?
+                    }
+                    _ => {}
+                }
+            }
+            Some(bundle) => bail!(
+                "{} is not inside {}, refusing to delete the folder",
+                source.display(),
+                bundle.display()
+            ),
+            None => remove_if_exists(&source)?,
+        }
     }
     refresh_menu();
     Ok(())
@@ -222,27 +478,57 @@ fn build_entry(kind: &Kind, target: &Path, id: &str) -> Result<DesktopEntry> {
     entry.set("Icon", &icon);
     entry.set(KEY_SOURCE, &target.to_string_lossy());
     entry.set(KEY_KIND, kind.label());
+    entry.set(KEY_IDENTITY, &identity::identify(target));
     entry.set(KEY_ARGS, &args);
     entry.set("Exec", &desktop::build_exec(target, &args));
     Ok(entry)
 }
 
-fn place(apps_dir: &Path, src: &Path) -> Result<PathBuf> {
+fn canonical(path: &Path) -> Result<PathBuf> {
+    path.canonicalize()
+        .with_context(|| format!("cannot access {}", path.display()))
+}
+
+fn prepare_apps_dir(apps_dir: &Path) -> Result<PathBuf> {
     fs::create_dir_all(apps_dir)
         .with_context(|| format!("cannot create {}", apps_dir.display()))?;
-    let apps_dir = apps_dir.canonicalize()?;
+    Ok(apps_dir.canonicalize()?)
-    if src.starts_with(&apps_dir) {
+}
-        return Ok(src.to_path_buf());
+
-    }
+fn file_name(path: &Path) -> Result<&OsStr> {
-    let dest = apps_dir.join(src.file_name().context("path has no file name")?);
+    path.file_name().context("path has no file name")
+}
+
+fn move_to(src: &Path, dest: &Path) -> Result<()> {
     if dest.exists() {
         bail!("{} already exists", dest.display());
     }
-    if fs::rename(src, &dest).is_err() {
+    if fs::rename(src, dest).is_ok() {
-        fs::copy(src, &dest).with_context(|| format!("cannot copy to {}", dest.display()))?;
+        return Ok(());
-        fs::remove_file(src).with_context(|| format!("cannot remove {}", src.display()))?;
+    }
+    copy_all(src, dest).with_context(|| format!("cannot copy to {}", dest.display()))?;
+    if src.is_dir() {
+        fs::remove_dir_all(src)
+    } else {
+        fs::remove_file(src)
+    }
+    .with_context(|| format!("cannot remove {}", src.display()))
+}
+
+fn copy_all(src: &Path, dest: &Path) -> io::Result<()> {
+    let meta = fs::symlink_metadata(src)?;
+    if meta.is_symlink() {
+        symlink(fs::read_link(src)?, dest)
+    } else if meta.is_dir() {
+        fs::create_dir(dest)?;
+        for entry in fs::read_dir(src)? {
+            let entry = entry?;
+            copy_all(&entry.path(), &dest.join(entry.file_name()))?;
+        }
+        fs::set_permissions(dest, meta.permissions())
+    } else {
+        fs::copy(src, dest).map(drop)
     }
-    Ok(dest)
 }
 
 fn make_executable(path: &Path) -> Result<()> {
@@ -302,6 +588,12 @@ fn file_stem(path: &Path) -> String {
         .unwrap_or_default()
 }
 
+fn modified(path: &Path) -> SystemTime {
+    fs::metadata(path)
+        .and_then(|m| m.modified())
+        .unwrap_or(SystemTime::UNIX_EPOCH)
+}
+
 fn remove_if_exists(path: &Path) -> Result<()> {
     match fs::remove_file(path) {
         Err(e) if e.kind() != io::ErrorKind::NotFound => {

src/thunar.rs

@@ -3,7 +3,9 @@ use std::{fs, path::PathBuf};
 use anyhow::{Context, Result};
 
 const SKELETON: &str = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<actions>\n</actions>\n";
-const IDS: [&str; 2] = ["ratbin-integrate", "ratbin-remove"];
+const IDS: [&str; 3] = ["ratbin-integrate", "ratbin-bundle", "ratbin-remove"];
+const FILE_CONDITIONS: &str = "\t<other-files/>\n\t<text-files/>\n";
+const ANY_CONDITIONS: &str = "\t<directories/>\n\t<audio-files/>\n\t<image-files/>\n\t<other-files/>\n\t<text-files/>\n\t<video-files/>\n";
 
 pub fn install() -> Result<PathBuf> {
     let exe = std::env::current_exe()?.canonicalize()?;
@@ -15,13 +17,23 @@ pub fn install() -> Result<PathBuf> {
             "application-x-executable",
             &format!("{exe} integrate --notify %F"),
             "Move to the applications folder and add a menu entry",
+            FILE_CONDITIONS,
         ),
         action(
             IDS[1],
+            "Integrate as bundle",
+            "folder-new",
+            &format!("{exe} bundle --notify %F"),
+            "Move the binary and the other selected files into their own folder and add a menu entry",
+            ANY_CONDITIONS,
+        ),
+        action(
+            IDS[2],
             "Remove menu integration",
             "edit-delete",
             &format!("{exe} remove --notify %F"),
             "Remove the menu entry created by ratbin",
+            ANY_CONDITIONS,
         ),
     ];
     let mut doc = stripped()?;
@@ -90,7 +102,14 @@ fn strip(doc: &str) -> String {
     out
 }
 
-fn action(id: &str, name: &str, icon: &str, command: &str, description: &str) -> String {
+fn action(
+    id: &str,
+    name: &str,
+    icon: &str,
+    command: &str,
+    description: &str,
+    conditions: &str,
+) -> String {
     format!(
         "<action>\n\
          \t<icon>{icon}</icon>\n\
@@ -101,8 +120,7 @@ fn action(id: &str, name: &str, icon: &str, command: &str, description: &str) ->
          \t<description>{description}</description>\n\
          \t<range></range>\n\
          \t<patterns>*</patterns>\n\
-         \t<other-files/>\n\
+         {conditions}\
-         \t<text-files/>\n\
          </action>\n",
         icon = xml_escape(icon),
         name = xml_escape(name),

src/tui.rs

@@ -1,4 +1,7 @@
-use std::{io, path::PathBuf};
+use std::{
+    io,
+    path::{Path, PathBuf},
+};
 
 use anyhow::Result;
 use ratatui::{
@@ -40,6 +43,7 @@ enum Mode {
     Browse,
     Edit(Form),
     Confirm,
+    Relink(Picker),
 }
 
 struct App {
@@ -59,7 +63,9 @@ impl App {
             status: None,
             quit: false,
         };
+        let repaired = store::repair();
         app.reload(None)?;
+        app.show_repairs(repaired);
         Ok(app)
     }
 
@@ -102,6 +108,13 @@ impl App {
                 KeyCode::Char('s') if ctrl => self.save(),
                 _ => form.on_key(key),
             },
+            Mode::Relink(picker) => match key.code {
+                KeyCode::Esc | KeyCode::Char('q') => self.mode = Mode::Browse,
+                KeyCode::Down | KeyCode::Char('j') => picker.list.select_next(),
+                KeyCode::Up | KeyCode::Char('k') => picker.list.select_previous(),
+                KeyCode::Enter => self.relink(),
+                _ => {}
+            },
         }
     }
 
@@ -122,9 +135,12 @@ impl App {
                     self.mode = Mode::Confirm;
                 }
             }
+            KeyCode::Char('f') => self.open_relink(),
             KeyCode::Char('r') => {
+                let repaired = store::repair();
                 let result = self.reload(None);
                 self.report(result.map(|()| "Reloaded".into()));
+                self.show_repairs(repaired);
             }
             _ => {}
         }
@@ -145,6 +161,52 @@ impl App {
         self.report(result.map(|()| format!("Removed {name}")));
     }
 
+    fn open_relink(&mut self) {
+        let Some(item) = self.selected() else {
+            return;
+        };
+        let current = item.source();
+        match store::relink_candidates(item) {
+            Ok(files) if files.is_empty() => {
+                self.status = Some(("No executables found next to this file".into(), true));
+            }
+            Ok(files) => {
+                let index = files.iter().position(|f| *f != current).unwrap_or(0);
+                self.mode = Mode::Relink(Picker {
+                    files,
+                    list: ListState::default().with_selected(Some(index)),
+                    current,
+                });
+            }
+            Err(e) => self.report(Err(e)),
+        }
+    }
+
+    fn relink(&mut self) {
+        let Mode::Relink(picker) = std::mem::replace(&mut self.mode, Mode::Browse) else {
+            return;
+        };
+        let Some(file) = picker.list.selected().and_then(|i| picker.files.get(i)) else {
+            return;
+        };
+        let Some(item) = self
+            .list
+            .selected()
+            .and_then(|index| self.items.get_mut(index))
+        else {
+            return;
+        };
+        let path = item.desktop_path.clone();
+        let name = item.name();
+        let result = store::relink(item, file);
+        let reloaded = self.reload(Some(path));
+        self.report(
+            result
+                .and(reloaded)
+                .map(|()| format!("{name} now starts {}", file_name(file))),
+        );
+    }
+
     fn save(&mut self) {
         let Mode::Edit(form) = std::mem::replace(&mut self.mode, Mode::Browse) else {
             return;
@@ -171,6 +233,18 @@ impl App {
         }
     }
 
+    fn show_repairs(&mut self, repaired: Result<Vec<Result<String>>>) {
+        match repaired {
+            Ok(results) => {
+                let fixed: Vec<String> = results.into_iter().filter_map(Result::ok).collect();
+                if !fixed.is_empty() {
+                    self.status = Some((format!("Repaired {}", fixed.join(", ")), false));
+                }
+            }
+            Err(e) => self.report(Err(e)),
+        }
+    }
+
     fn report(&mut self, result: Result<String>) {
         self.status = Some(match result {
             Ok(message) => (message, false),
@@ -211,10 +285,11 @@ impl App {
         frame.render_widget(self.details(), right);
         frame.render_widget(self.footer(), footer);
 
-        match &self.mode {
+        match &mut self.mode {
             Mode::Browse => {}
             Mode::Edit(form) => form.draw(frame, main),
             Mode::Confirm => self.draw_confirm(frame, main),
+            Mode::Relink(picker) => picker.draw(frame, main),
         }
     }
 
@@ -250,10 +325,13 @@ impl App {
             row("File", source.display().to_string()),
             row("Entry", item.desktop_path.display().to_string()),
         ];
+        if let Some(bundle) = item.bundle() {
+            lines.insert(lines.len() - 1, row("Folder", bundle.display().to_string()));
+        }
         if !source.exists() {
             lines.push(Line::default());
             lines.push(Line::styled(
-                "The file no longer exists, so this menu entry is broken.",
+                "The file no longer exists, so this menu entry is broken. Press f to choose its new file.",
                 Style::default().fg(Color::Red),
             ));
         }
@@ -268,9 +346,10 @@ impl App {
             return Line::styled(message.clone(), Style::default().fg(color));
         }
         let hints = match self.mode {
-            Mode::Browse => "↑↓ select  enter edit  d remove  r reload  q quit",
+            Mode::Browse => "↑↓ select  enter edit  f change file  d remove  r reload  q quit",
             Mode::Edit(_) => "tab/↑↓ field  space toggle  ctrl+u clear  enter save  esc cancel",
             Mode::Confirm => "e entry only  d entry + file  esc cancel",
+            Mode::Relink(_) => "↑↓ select  enter use this file  esc cancel",
         };
         Line::styled(hints, Style::default().fg(Color::DarkGray))
     }
@@ -279,11 +358,11 @@ impl App {
         let Some(item) = self.selected() else {
             return;
         };
-        let file_name = item
+        let (path, suffix) = match item.bundle() {
-            .source()
+            Some(bundle) => (bundle, "/ and everything in it"),
-            .file_name()
+            None => (item.source(), ""),
-            .map(|n| n.to_string_lossy().into_owned())
+        };
-            .unwrap_or_default();
+        let file_name = file_name(&path);
         let rect = popup(area, 64, 6);
         frame.render_widget(Clear, rect);
         frame.render_widget(
@@ -291,7 +370,7 @@ impl App {
                 Line::from(format!("Remove \"{}\"?", item.name())),
                 Line::default(),
                 Line::from("e  remove the menu entry only"),
-                Line::from(format!("d  also delete {file_name}")),
+                Line::from(format!("d  also delete {file_name}{suffix}")),
             ])
             .block(
                 Block::bordered()
@@ -303,6 +382,44 @@ impl App {
     }
 }
 
+struct Picker {
+    files: Vec<PathBuf>,
+    list: ListState,
+    current: PathBuf,
+}
+
+impl Picker {
+    fn draw(&mut self, frame: &mut Frame, area: Rect) {
+        let rect = popup(area, 80, self.files.len() as u16 + 2);
+        frame.render_widget(Clear, rect);
+        let dir = self
+            .files
+            .first()
+            .and_then(|file| file.parent())
+            .map(|dir| dir.display().to_string())
+            .unwrap_or_default();
+        let items: Vec<ListItem> = self
+            .files
+            .iter()
+            .map(|file| {
+                let mut spans = vec![Span::raw(file_name(file))];
+                if *file == self.current {
+                    spans.push(Span::styled(
+                        "  current",
+                        Style::default().fg(Color::DarkGray),
+                    ));
+                }
+                ListItem::new(Line::from(spans))
+            })
+            .collect();
+        let list = List::new(items)
+            .block(Block::bordered().title(format!(" Choose the file in {dir} ")))
+            .highlight_style(Style::default().add_modifier(Modifier::REVERSED))
+            .highlight_symbol("› ");
+        frame.render_stateful_widget(list, rect, &mut self.list);
+    }
+}
+
 struct Form {
     inputs: [Input; 5],
     terminal: bool,
@@ -451,6 +568,12 @@ impl Input {
     }
 }
 
+fn file_name(path: &Path) -> String {
+    path.file_name()
+        .map(|n| n.to_string_lossy().into_owned())
+        .unwrap_or_default()
+}
+
 fn popup(area: Rect, width: u16, height: u16) -> Rect {
     let width = width.min(area.width);
     let height = height.min(area.height);