Make bun pm ls list installed packages instead of lockfile entries

completions/bun-cli.json

@@ -3368,7 +3368,7 @@
         },
         "ls": {
           "name": "ls",
-          "description": "list the dependency tree according to the current lockfile",
+          "description": "list the tree of installed dependencies",
           "flags": [],
           "positionalArgs": []
         },

completions/bun.zsh

@@ -259,7 +259,7 @@ _bun_pm_completion() {
     cmd2)
         sub_commands=(
             'bin\:"print the path to bin folder" '
-            'ls\:"list the dependency tree according to the current lockfile" '
+            'ls\:"list the tree of installed dependencies" '
             'licenses\:"list installed packages grouped by license" '
             'hash\:"generate & print the hash of the current lockfile" '
             'hash-string\:"print the string used to hash the lockfile" '
@@ -295,7 +295,7 @@ _bun_pm_completion() {
             ;;
         ls)
             pmargs=(
-                "--all[list the entire dependency tree according to the current lockfile]"
+                "--all[list the entire tree of installed dependencies]"
                 "--trusted[list only trusted dependencies]"
             )
 

src/install/PackageManager.rs

@@ -134,8 +134,8 @@ impl PackageManagerCommand {
   <d>└<r> <cyan>--quiet<r>                   only output the tarball filename
   <b><green>bun pm<r> <blue>bin<r>                  print the path to bin folder
   <d>└<r> <cyan>-g<r>                        print the <b>global<r> path to bin folder
-  <b><green>bun pm<r> <blue>ls<r>                   list the dependency tree according to the current lockfile
-  <d>├<r> <cyan>--all<r>                     list the entire dependency tree according to the current lockfile
+  <b><green>bun pm<r> <blue>ls<r>                   list the tree of installed dependencies
+  <d>├<r> <cyan>--all<r>                     list the entire tree of installed dependencies
   <d>└<r> <cyan>--trusted<r>                 list only trusted dependencies
   <b><green>bun pm<r> <blue>why<r> <d>\<pkg\><r>            show dependency tree explaining why a package is installed
   <b><green>bun pm<r> <blue>licenses<r>             list installed packages grouped by license

src/runtime/cli/mod.rs

@@ -2260,7 +2260,7 @@ Full documentation is available at <magenta>https://bun.com/docs/cli/why<r>
 
 <b>Commands:<r>
   <b><green>bun pm<r> <blue>bin<r>              print the path to bin folder
-  <b><green>bun pm<r> <blue>ls<r>               list the dependency tree according to the current lockfile
+  <b><green>bun pm<r> <blue>ls<r>               list the tree of installed dependencies
   <b><green>bun pm<r> <blue>whoami<r>           print the current npm username
   <b><green>bun pm<r> <blue>hash<r>             generate & print the hash of the current lockfile
   <b><green>bun pm<r> <blue>cache<r>            print the path to the cache folder

src/runtime/cli/package_manager_command.rs

@@ -12,14 +12,14 @@ use bun_install::package_manager_real::{
     CommandLineArguments, Subcommand, fetch_cache_directory_path, get_cache_directory,
     package_manager_options::LogLevel, setup_global_dir,
 };
-use bun_install::{DependencyID, PackageID, PackageManager, migration};
-use bun_paths::{self as Path, PathBuffer};
+use bun_install::{DependencyID, PackageID, PackageManager, ResolutionTag, migration};
+use bun_paths::{self as Path, AutoAbsPath, PathBuffer};
 use bun_resolver::fs as Fs;
 use bun_sys::{self, Dir, Fd, File};
 
 use crate::cli::Command;
 use crate::cli::pm_diff_command as PmDiffCommand;
-use crate::cli::pm_licenses_command::{LicensesFlags, PmLicensesCommand};
+use crate::cli::pm_licenses_command::{BunStore, LicensesFlags, PmLicensesCommand};
 use crate::cli::pm_pkg_command::PmPkgCommand;
 use crate::cli::pm_trusted_command::{DefaultTrustedCommand, TrustCommand, UntrustedCommand};
 use crate::cli::pm_version_command::PmVersionCommand;
@@ -38,6 +38,83 @@ pub(crate) struct NodeModulesFolder {
     dependencies: Box<[DependencyID]>,
 }
 
+/// Disk-existence check for `bun pm ls`: the lockfile also contains entries
+/// that were never installed (platform-mismatched optionals) or were removed
+/// after install (`bun prune --production`), and those must not be listed as
+/// the contents of `node_modules`.
+struct InstalledFilter {
+    path: AutoAbsPath,
+    top_len: usize,
+    store: BunStore,
+}
+
+impl InstalledFilter {
+    fn init() -> Self {
+        let path = AutoAbsPath::init_top_level_dir();
+        let top_len = path.len();
+        Self {
+            path,
+            top_len,
+            store: BunStore::init(),
+        }
+    }
+
+    fn node_modules_exists(&mut self) -> bool {
+        self.path.set_length(self.top_len);
+        let _ = self.path.append(b"node_modules");
+        let exists = bun_sys::exists(self.path.slice());
+        self.path.set_length(self.top_len);
+        exists
+    }
+
+    fn is_installed(
+        &mut self,
+        lockfile: &Lockfile,
+        relative_path: &[u8],
+        dep_id: DependencyID,
+    ) -> bool {
+        let package_id = lockfile.buffers.resolutions.as_slice()[dep_id as usize];
+        if package_id as usize >= lockfile.packages.len() {
+            return false;
+        }
+        let slice = lockfile.packages.slice();
+        let resolution = &slice.items_resolution()[package_id as usize];
+        // Local sources (the project itself, workspaces, `bun link`ed packages)
+        // always exist on disk outside of node_modules.
+        if matches!(
+            resolution.tag,
+            ResolutionTag::Root | ResolutionTag::Workspace | ResolutionTag::Symlink
+        ) {
+            return true;
+        }
+
+        let buf = lockfile.buffers.string_bytes.as_slice();
+        let alias = lockfile.buffers.dependencies.as_slice()[dep_id as usize]
+            .name
+            .slice(buf);
+        self.path.set_length(self.top_len);
+        let _ = self.path.append(relative_path);
+        let _ = self.path.append(alias);
+        let exists = bun_sys::exists(self.path.slice());
+        self.path.set_length(self.top_len);
+        if exists {
+            return true;
+        }
+
+        // Isolated installs (`node_modules/.bun`) only link direct dependencies
+        // into each package's node_modules; transitive packages live in the store.
+        self.store
+            .lookup(
+                &mut self.path,
+                self.top_len,
+                slice.items_name()[package_id as usize],
+                resolution,
+                buf,
+            )
+            .is_some()
+    }
+}
+
 // Transient sort-comparator context; lifetime is fn-local.
 struct ByName<'a> {
     dependencies: &'a [Dependency],
@@ -186,8 +263,8 @@ impl PackageManagerCommand {
   <d>└<r> <cyan>--quiet<r>                   only output the tarball filename\n\
   <b><green>bun pm<r> <blue>bin<r>                  print the path to bin folder\n\
   <d>└<r> <cyan>-g<r>                        print the <b>global<r> path to bin folder\n\
-  <b><green>bun pm<r> <blue>ls<r>                   list the dependency tree according to the current lockfile\n\
-  <d>├<r> <cyan>--all<r>                     list the entire dependency tree according to the current lockfile\n\
+  <b><green>bun pm<r> <blue>ls<r>                   list the tree of installed dependencies\n\
+  <d>├<r> <cyan>--all<r>                     list the entire tree of installed dependencies\n\
   <d>└<r> <cyan>--trusted<r>                 list only trusted dependencies\n\
   <b><green>bun pm<r> <blue>why<r> <d>\\<pkg\\><r>            show dependency tree explaining why a package is installed\n\
   <b><green>bun pm<r> <blue>diff<r> <d>[a] [b]<r>           show what changed between two versions of a package (or vs a folder/tarball)\n\
@@ -563,10 +640,21 @@ Learn more about these at <magenta>https://bun.com/docs/cli/pm<r>.\n";
             Output::flush();
             Output::disable_buffering();
             let lockfile: &Lockfile = &pm.lockfile;
+
+            let mut installed = InstalledFilter::init();
+            if !installed.node_modules_exists() {
+                if log_level != LogLevel::Silent {
+                    Output::err_generic("node_modules not found, nothing to list", ());
+                    bun_core::note!("run 'bun install' first");
+                }
+                Global::exit(1);
+            }
+
             let mut iterator =
                 tree::Iterator::<{ tree::IteratorPathStyle::NodeModules }>::init(lockfile);
 
             let mut max_depth: usize = 0;
+            let mut installed_count: usize = 0;
 
             let mut directories: Vec<NodeModulesFolder> = Vec::new();
             while let Some(node_modules) = iterator.next(None) {
@@ -575,7 +663,19 @@ Learn more about these at <magenta>https://bun.com/docs/cli/pm<r>.\n";
                 path.extend_from_slice(node_modules.relative_path.as_bytes());
                 path.push(0);
 
-                let dependencies: Box<[DependencyID]> = Box::from(node_modules.dependencies);
+                let dependencies: Box<[DependencyID]> = node_modules
+                    .dependencies
+                    .iter()
+                    .copied()
+                    .filter(|&dep_id| {
+                        installed.is_installed(
+                            lockfile,
+                            node_modules.relative_path.as_bytes(),
+                            dep_id,
+                        )
+                    })
+                    .collect();
+                installed_count += dependencies.len();
 
                 if max_depth < node_modules.depth + 1 {
                     max_depth = node_modules.depth + 1;
@@ -638,7 +738,7 @@ Learn more about these at <magenta>https://bun.com/docs/cli/pm<r>.\n";
                 Output::println(format_args!(
                     "{} node_modules ({})",
                     bstr::BStr::new(path),
-                    lockfile.buffers.hoisted_dependencies.len(),
+                    installed_count,
                 ));
                 let string_bytes = lockfile.buffers.string_bytes.as_slice();
                 let mut sorted_dependencies: Vec<DependencyID> =
@@ -654,6 +754,9 @@ Learn more about these at <magenta>https://bun.com/docs/cli/pm<r>.\n";
                 index_sort::sort_indices(&mut sorted_dependencies, &mut |a, b| by_name.cmp(a, b));
                 sorted_dependencies.dedup_by(|a, b| by_name.cmp(*a, *b) == Ordering::Equal);
 
+                sorted_dependencies
+                    .retain(|&dep_id| installed.is_installed(lockfile, b"node_modules", dep_id));
+
                 if trusted_only {
                     sorted_dependencies.retain(|&dep_id| {
                         let package_id = lockfile.buffers.resolutions.as_slice()[dep_id as usize];

src/runtime/cli/pm_licenses_command.rs

@@ -44,7 +44,7 @@ struct Entry {
 }
 
 /// Lazily-scanned, sorted entry names of `node_modules/.bun/`; `None` until first needed.
-struct BunStore {
+pub(crate) struct BunStore {
     entries: Option<Vec<Box<[u8]>>>,
 }
 
@@ -197,7 +197,7 @@ impl PmLicensesCommand {
         let buf = lockfile.buffers.string_bytes.as_slice();
 
         let mut log = Log::init();
-        let mut store = BunStore { entries: None };
+        let mut store = BunStore::init();
         let mut disk = DiskIndex { entries: None };
         let mut entries: Vec<Entry> = Vec::new();
         let mut missing: usize = 0;
@@ -523,6 +523,10 @@ fn author_of(json: &Expr) -> Option<Box<[u8]>> {
 }
 
 impl BunStore {
+    pub(crate) fn init() -> Self {
+        Self { entries: None }
+    }
+
     fn read_info(
         &mut self,
         path: &mut AutoAbsPath,
@@ -543,7 +547,7 @@ impl BunStore {
         read_package_info_at(path, top_len, &segments, log)
     }
 
-    fn lookup(
+    pub(crate) fn lookup(
         &mut self,
         path: &mut AutoAbsPath,
         top_len: usize,

test/cli/bun.test.ts

@@ -259,7 +259,7 @@ describe("bun", () => {
         "bun pm --help",
         ["pm"],
         [
-          /^ {2}bun pm ls +list the dependency tree according to the current lockfile$/m,
+          /^ {2}bun pm ls +list the tree of installed dependencies$/m,
           /^ {2}bun pm licenses +list installed packages grouped by license$/m,
         ],
       ],