diff --git a/lib/cli/src/cli.rs b/lib/cli/src/cli.rs
index f580175f5..5b06d554b 100644
--- a/lib/cli/src/cli.rs
+++ b/lib/cli/src/cli.rs
@@ -14,6 +14,7 @@ use crate::commands::{Cache, Config, Inspect, Run, RunWithoutFile, SelfUpdate, V
 use crate::error::PrettyError;
 use clap::{CommandFactory, ErrorKind, Parser};
 use spinner::SpinnerHandle;
+use std::fmt;
 use wasmer_registry::{get_all_local_packages, PackageDownloadInfo};
 
 #[derive(Parser, Debug)]
@@ -37,7 +38,6 @@ use wasmer_registry::{get_all_local_packages, PackageDownloadInfo};
 )]
 /// The options for the wasmer Command Line Interface
 enum WasmerCLIOptions {
-
     /// List all locally installed packages
     #[clap(name = "list")]
     List,
@@ -253,11 +253,41 @@ fn try_run_package_or_file(args: &[String], r: &Run) -> Result<(), anyhow::Error
 
     let package = format!("{}", r.path.display());
 
+    let mut is_fake_sv = false;
     let mut sv = match split_version(&package) {
         Ok(o) => o,
-        Err(_) => return r.execute(),
+        Err(_) => {
+            let mut fake_sv = SplitVersion {
+                package: package.to_string(),
+                version: None,
+                command: None,
+            };
+            is_fake_sv = true;
+            match try_lookup_command(&mut fake_sv) {
+                Ok(o) => SplitVersion {
+                    package: o.package,
+                    version: Some(o.version),
+                    command: r.command_name.clone(),
+                },
+                Err(e) => {
+                    return Err(
+                        anyhow::anyhow!("No package for command {package:?} found, file {package:?} not found either")
+                        .context(e)
+                        .context(anyhow::anyhow!("{}", r.path.display()))
+                    );
+                }
+            }
+        }
     };
 
+    if sv.command.is_none() {
+        sv.command = r.command_name.clone();
+    }
+
+    if sv.command.is_none() && is_fake_sv {
+        sv.command = Some(package.to_string());
+    }
+
     let mut package_download_info = None;
     if !sv.package.contains('/') {
         if let Ok(o) = try_lookup_command(&mut sv) {
@@ -289,7 +319,7 @@ fn try_lookup_command(sv: &mut SplitVersion) -> Result<PackageDownloadInfo, anyh
     }
 
     sp.close();
-    Err(anyhow::anyhow!("command {sv:?} not found"))
+    Err(anyhow::anyhow!("command {sv} not found"))
 }
 
 fn try_execute_local_package(args: &[String], sv: &SplitVersion) -> Result<(), anyhow::Error> {
@@ -303,6 +333,7 @@ fn try_execute_local_package(args: &[String], sv: &SplitVersion) -> Result<(), a
         &package.registry,
         &package.name,
         &package.version,
+        sv.command.as_ref().map(|s| s.as_str()),
     )
     .map_err(|e| anyhow!("{e}"))?;
 
@@ -310,11 +341,22 @@ fn try_execute_local_package(args: &[String], sv: &SplitVersion) -> Result<(), a
     let mut args_without_package = args.to_vec();
     args_without_package.remove(1);
 
-    let mut run_args = RunWithoutFile::try_parse_from(args_without_package.iter())?;
-    run_args.command_name = sv.command.clone();
-    run_args
-        .into_run_args(local_package_wasm_path, Some(package.manifest))
+    if args_without_package.get(1) == Some(&sv.package)
+        || args_without_package.get(1) == sv.command.as_ref()
+    {
+        args_without_package.remove(1);
+    }
+
+    if args_without_package.get(0) == Some(&sv.package)
+        || args_without_package.get(0) == sv.command.as_ref()
+    {
+        args_without_package.remove(0);
+    }
+
+    RunWithoutFile::try_parse_from(args_without_package.iter())?
+        .into_run_args(local_package_wasm_path.clone(), Some(package.manifest))
         .execute()
+        .map_err(|e| e.context(anyhow::anyhow!("{}", local_package_wasm_path.display())))
 }
 
 fn try_autoinstall_package(
@@ -362,6 +404,22 @@ struct SplitVersion {
     command: Option<String>,
 }
 
+impl fmt::Display for SplitVersion {
+    fn fmt(&self, f: &mut fmt::Formatter) -> fmt::Result {
+        let version = self
+            .version
+            .as_ref()
+            .map(|s| s.as_str())
+            .unwrap_or("latest");
+        let command = self
+            .command
+            .as_ref()
+            .map(|s| format!(":{s}"))
+            .unwrap_or_default();
+        write!(f, "{}@{version}{command}", self.package)
+    }
+}
+
 #[test]
 fn test_split_version() {
     assert_eq!(
@@ -401,6 +459,9 @@ fn split_version(s: &str) -> Result<SplitVersion, anyhow::Error> {
     let re1 = regex::Regex::new(r#"(.*)/(.*)@(.*):(.*)"#).unwrap();
     let re2 = regex::Regex::new(r#"(.*)/(.*)@(.*)"#).unwrap();
     let re3 = regex::Regex::new(r#"(.*)/(.*)"#).unwrap();
+    let re4 = regex::Regex::new(r#"(.*)/(.*):(.*)"#).unwrap();
+
+    let mut no_version = false;
 
     let captures = if re1.is_match(s) {
         re1.captures(s)
@@ -420,6 +481,16 @@ fn split_version(s: &str) -> Result<SplitVersion, anyhow::Error> {
                     .collect::<Vec<_>>()
             })
             .unwrap_or_default()
+    } else if re4.is_match(s) {
+        no_version = true;
+        re4.captures(s)
+            .map(|c| {
+                c.iter()
+                    .flatten()
+                    .map(|m| m.as_str().to_owned())
+                    .collect::<Vec<_>>()
+            })
+            .unwrap_or_default()
     } else if re3.is_match(s) {
         re3.captures(s)
             .map(|c| {
@@ -449,8 +520,12 @@ fn split_version(s: &str) -> Result<SplitVersion, anyhow::Error> {
 
     let sv = SplitVersion {
         package: format!("{namespace}/{name}"),
-        version: captures.get(3).cloned(),
-        command: captures.get(4).cloned(),
+        version: if no_version {
+            None
+        } else {
+            captures.get(3).cloned()
+        },
+        command: captures.get(if no_version { 3 } else { 4 }).cloned(),
     };
 
     let svp = sv.package.clone();
diff --git a/lib/cli/src/commands/run.rs b/lib/cli/src/commands/run.rs
index 0e0d88e34..5244ea69b 100644
--- a/lib/cli/src/commands/run.rs
+++ b/lib/cli/src/commands/run.rs
@@ -5,6 +5,7 @@ use crate::store::{CompilerType, StoreOptions};
 use crate::suggestions::suggest_function_exports;
 use crate::warning;
 use anyhow::{anyhow, Context, Result};
+use std::collections::BTreeMap;
 use std::ops::Deref;
 use std::path::PathBuf;
 use std::str::FromStr;
@@ -81,6 +82,9 @@ pub struct RunWithoutFile {
 impl RunWithoutFile {
     /// Given a local path, returns the `Run` command (overriding the `--path` argument).
     pub fn into_run_args(mut self, pathbuf: PathBuf, manifest: Option<wapm_toml::Manifest>) -> Run {
+        #[cfg(feature = "wasi")]
+        let mut wasi_map_dir = Vec::new();
+
         #[cfg(feature = "wasi")]
         {
             let pkg_fs = match pathbuf.parent() {
@@ -92,13 +96,13 @@ impl RunWithoutFile {
                 .and_then(|m| m.package.pkg_fs_mount_point.clone())
             {
                 if m == "." {
-                    self.wasi.map_dir("/", pkg_fs);
+                    wasi_map_dir.push(("/".to_string(), pkg_fs));
                 } else {
                     if m.starts_with('.') {
                         m = format!("{}{}", pkg_fs.display(), &m[1..]);
                     }
                     let path = std::path::Path::new(&m).to_path_buf();
-                    self.wasi.map_dir("/", path);
+                    wasi_map_dir.push(("/".to_string(), path));
                 }
             }
         }
@@ -123,7 +127,7 @@ impl RunWithoutFile {
                     continue;
                 }
                 let alias_pathbuf = std::path::Path::new(&real_dir).to_path_buf();
-                self.wasi.map_dir(alias, alias_pathbuf.clone());
+                wasi_map_dir.push((alias.to_string(), alias_pathbuf.clone()));
 
                 fn is_dir(e: &walkdir::DirEntry) -> bool {
                     let meta = match e.metadata() {
@@ -142,12 +146,34 @@ impl RunWithoutFile {
                     let pathbuf = entry.path().canonicalize().unwrap();
                     let path = format!("{}", pathbuf.display());
                     let relativepath = path.replacen(&root_display, "", 1);
-                    self.wasi
-                        .map_dir(&format!("/{alias}{relativepath}"), pathbuf);
+                    wasi_map_dir.push((format!("/{alias}{relativepath}"), pathbuf));
                 }
             }
         }
 
+        // If a directory is mapped twice, the WASI runtime will throw an error
+        // We need to calculate the "key" path, then deduplicate the mapping
+        #[cfg(feature = "wasi")]
+        {
+            let parent = match pathbuf.parent() {
+                Some(parent) => parent.to_path_buf(),
+                None => pathbuf.clone(),
+            };
+            let mut wasi_map = BTreeMap::new();
+            for (k, v) in wasi_map_dir {
+                let path_v = v.canonicalize().unwrap_or(v.clone());
+                let mut k_path = std::path::Path::new(&k).to_path_buf();
+                if k_path.is_relative() {
+                    k_path = parent.join(&k);
+                }
+                let key = format!("{}", k_path.canonicalize().unwrap_or(k_path).display());
+                wasi_map.insert(key, (k, path_v));
+            }
+            for (_, (k, v)) in wasi_map {
+                self.wasi.map_dir(&k, v);
+            }
+        }
+
         Run {
             path: pathbuf,
             options: RunWithoutFile {
@@ -155,7 +181,10 @@ impl RunWithoutFile {
                 #[cfg(feature = "cache")]
                 disable_cache: self.disable_cache,
                 invoke: self.invoke,
-                command_name: self.command_name,
+                // If the RunWithoutFile was constructed via a package name,
+                // the correct syntax is "package:command-name" (--command-name would be
+                // interpreted as a CLI argument for the .wasm file)
+                command_name: None,
                 #[cfg(feature = "cache")]
                 cache_key: self.cache_key,
                 store: self.store,
diff --git a/lib/registry/src/lib.rs b/lib/registry/src/lib.rs
index 89a23e517..5fe0dc68b 100644
--- a/lib/registry/src/lib.rs
+++ b/lib/registry/src/lib.rs
@@ -561,6 +561,7 @@ pub fn get_package_local_wasm_file(
     registry_host: &str,
     name: &str,
     version: &str,
+    command: Option<&str>,
 ) -> Result<PathBuf, String> {
     let dir = get_package_local_dir(registry_host, name, version)?;
     let wapm_toml_path = dir.join("wapm.toml");
@@ -570,14 +571,17 @@ pub fn get_package_local_wasm_file(
         .map_err(|e| format!("cannot parse wapm.toml for {name}@{version}: {e}"))?;
 
     // TODO: this will just return the path for the first command, so this might not be correct
-    let module_name = wapm
-        .command
-        .unwrap_or_default()
-        .first()
-        .map(|m| m.get_module())
-        .ok_or_else(|| {
-            format!("cannot get entrypoint for {name}@{version}: package has no commands")
-        })?;
+    let module_name = match command {
+        Some(s) => s.to_string(),
+        None => wapm
+            .command
+            .unwrap_or_default()
+            .first()
+            .map(|m| m.get_module())
+            .ok_or_else(|| {
+                format!("cannot get entrypoint for {name}@{version}: package has no commands")
+            })?,
+    };
 
     let wasm_file_name = wapm
         .module