clean up cmd line

add.ce

@@ -1,18 +1,43 @@
-// cell add <locator> [alias] - Add and install a package with its dependencies
+// cell add <locator> [alias] - Add a dependency to the current package
+//
+// Usage:
+//   cell add <locator>         Add a dependency using default alias
+//   cell add <locator> <alias> Add a dependency with custom alias
+//
+// This adds the dependency to cell.toml and installs it to the shop.
 
 var shop = use('internal/shop')
+var pkg = use('package')
+var build = use('build')
 var fd = use('fd')
 
-if (args.length < 1) {
-  log.console("Usage: cell add <locator> [alias]")
-  log.console("Examples:")
-  log.console("  cell add gitea.pockle.world/john/prosperon@main")
-  log.console("  cell add github.com/user/repo@v1.0.0 myalias")
-  $stop()
-  return
+var locator = null
+var alias = null
+
+for (var i = 0; i < args.length; i++) {
+  if (args[i] == '--help' || args[i] == '-h') {
+    log.console("Usage: cell add <locator> [alias]")
+    log.console("")
+    log.console("Add a dependency to the current package.")
+    log.console("")
+    log.console("Examples:")
+    log.console("  cell add gitea.pockle.world/john/prosperon")
+    log.console("  cell add gitea.pockle.world/john/cell-image image")
+    log.console("  cell add ../local-package")
+    $stop()
+  } else if (!args[i].startsWith('-')) {
+    if (!locator) {
+      locator = args[i]
+    } else if (!alias) {
+      alias = args[i]
+    }
+  }
 }
 
-var locator = args[0]
+if (!locator) {
+  log.console("Usage: cell add <locator> [alias]")
+  $stop()
+}
 
 // Resolve relative paths to absolute paths
 if (locator == '.' || locator.startsWith('./') || locator.startsWith('../') || fd.is_dir(locator)) {
@@ -21,8 +46,58 @@ if (locator == '.' || locator.startsWith('./') || locator.startsWith('../') || f
     locator = resolved
   }
 }
-var alias = args.length > 1 ? args[1] : null
 
-shop.get(locator, alias)
+// Generate default alias from locator
+if (!alias) {
+  // Use the last component of the locator as alias
+  var parts = locator.split('/')
+  alias = parts[parts.length - 1]
+  // Remove any version suffix
+  if (alias.includes('@')) {
+    alias = alias.split('@')[0]
+  }
+}
 
-$stop()
+// Check we're in a package directory
+var cwd = fd.realpath('.')
+if (!fd.is_file(cwd + '/cell.toml')) {
+  log.error("Not in a package directory (no cell.toml found)")
+  $stop()
+}
+
+log.console("Adding " + locator + " as '" + alias + "'...")
+
+// Add to local project's cell.toml
+try {
+  pkg.add_dependency(null, locator, alias)
+  log.console("  Added to cell.toml")
+} catch (e) {
+  log.error("Failed to update cell.toml: " + e)
+  $stop()
+}
+
+// Install to shop
+try {
+  shop.get(locator)
+  shop.extract(locator)
+
+  // Build scripts
+  shop.build_package_scripts(locator)
+
+  // Build C code if any
+  try {
+    var target = build.detect_host_target()
+    build.build_dynamic(locator, target, 'release')
+  } catch (e) {
+    // Not all packages have C code
+  }
+
+  log.console("  Installed to shop")
+} catch (e) {
+  log.error("Failed to install: " + e)
+  $stop()
+}
+
+log.console("Added " + alias + " (" + locator + ")")
+
+$stop()

build.ce

@@ -1,9 +1,11 @@
-// cell build [options] - Build dynamic libraries locally for the current machine
+// cell build [<locator>] - Build dynamic libraries locally for the current machine
 //
 // Usage:
-//   cell build                Build dynamic libraries for all packages
-//   cell build -p <pkg>       Build dynamic library for specific package
+//   cell build                Build dynamic libraries for all packages in shop
+//   cell build .              Build dynamic library for current directory package
+//   cell build <locator>      Build dynamic library for specific package
 //   cell build -t <target>    Cross-compile dynamic libraries for target platform
+//   cell build -b <type>      Build type: release (default), debug, or minsize
 
 var build = use('build')
 var shop = use('internal/shop')
@@ -12,7 +14,9 @@ var fd = use('fd')
 
 var target = null
 var target_package = null
-var buildtype = 'debug'
+var buildtype = 'release'
+var force_rebuild = false
+var dry_run = false
 
 for (var i = 0; i < args.length; i++) {
   if (args[i] == '-t' || args[i] == '--target') {
@@ -23,6 +27,7 @@ for (var i = 0; i < args.length; i++) {
       $stop()
     }
   } else if (args[i] == '-p' || args[i] == '--package') {
+    // Legacy support for -p flag
     if (i + 1 < args.length) {
       target_package = args[++i]
     } else {
@@ -40,6 +45,10 @@ for (var i = 0; i < args.length; i++) {
       log.error('-b requires a buildtype (release, debug, minsize)')
       $stop()
     }
+  } else if (args[i] == '--force') {
+    force_rebuild = true
+  } else if (args[i] == '--dry-run') {
+    dry_run = true
   } else if (args[i] == '--list-targets') {
     log.console('Available targets:')
     var targets = build.list_targets()
@@ -47,6 +56,19 @@ for (var i = 0; i < args.length; i++) {
       log.console('  ' + targets[t])
     }
     $stop()
+  } else if (!args[i].startsWith('-') && !target_package) {
+    // Positional argument - treat as package locator
+    target_package = args[i]
+  }
+}
+
+// Resolve local paths to absolute paths
+if (target_package) {
+  if (target_package == '.' || target_package.startsWith('./') || target_package.startsWith('../') || fd.is_dir(target_package)) {
+    var resolved = fd.realpath(target_package)
+    if (resolved) {
+      target_package = resolved
+    }
   }
 }
 

clean.ce

@@ -1,26 +1,218 @@
-// cell clean - Remove build artifacts from global shop
+// cell clean [<scope>] - Remove cached material to force refetch/rebuild
+//
+// Usage:
+//   cell clean              Clean build outputs for current directory package
+//   cell clean .            Clean build outputs for current directory package
+//   cell clean <locator>    Clean build outputs for specific package
+//   cell clean shop         Clean entire shop
+//   cell clean world        Clean all world packages
+//
+// Options:
+//   --build      Remove build outputs only (default)
+//   --fetch      Remove fetched sources only
+//   --all        Remove both build outputs and fetched sources
+//   --deep       Apply to full dependency closure
+//   --dry-run    Show what would be deleted
 
-var fd = use('fd')
 var shop = use('internal/shop')
+var pkg = use('package')
+var fd = use('fd')
 
-var build_dir = shop.get_shop_path() + '/build'
+var scope = null
+var clean_build = false
+var clean_fetch = false
+var deep = false
+var dry_run = false
 
-if (!fd.is_dir(build_dir)) {
-  log.console("No build directory found at " + build_dir)
-  $stop()
-  return
+for (var i = 0; i < args.length; i++) {
+  if (args[i] == '--build') {
+    clean_build = true
+  } else if (args[i] == '--fetch') {
+    clean_fetch = true
+  } else if (args[i] == '--all') {
+    clean_build = true
+    clean_fetch = true
+  } else if (args[i] == '--deep') {
+    deep = true
+  } else if (args[i] == '--dry-run') {
+    dry_run = true
+  } else if (args[i] == '--help' || args[i] == '-h') {
+    log.console("Usage: cell clean [<scope>] [options]")
+    log.console("")
+    log.console("Remove cached material to force refetch/rebuild.")
+    log.console("")
+    log.console("Scopes:")
+    log.console("  <locator>  Clean specific package")
+    log.console("  shop       Clean entire shop")
+    log.console("  world      Clean all world packages")
+    log.console("")
+    log.console("Options:")
+    log.console("  --build    Remove build outputs only (default)")
+    log.console("  --fetch    Remove fetched sources only")
+    log.console("  --all      Remove both build outputs and fetched sources")
+    log.console("  --deep     Apply to full dependency closure")
+    log.console("  --dry-run  Show what would be deleted")
+    $stop()
+  } else if (!args[i].startsWith('-')) {
+    scope = args[i]
+  }
 }
 
-log.console("Cleaning build artifacts...")
-
-// Remove the build directory
-try {
-  fd.rm(build_dir)
-  log.console("Build directory removed: " + build_dir)
-} catch (e) {
-  log.error(e)
+// Default to --build if nothing specified
+if (!clean_build && !clean_fetch) {
+  clean_build = true
 }
 
-log.console("Clean complete!")
+// Default scope to current directory
+if (!scope) {
+  scope = '.'
+}
 
-$stop()
+// Resolve local paths for single package scope
+var is_shop_scope = (scope == 'shop')
+var is_world_scope = (scope == 'world')
+
+if (!is_shop_scope && !is_world_scope) {
+  if (scope == '.' || scope.startsWith('./') || scope.startsWith('../') || fd.is_dir(scope)) {
+    var resolved = fd.realpath(scope)
+    if (resolved) {
+      scope = resolved
+    }
+  }
+}
+
+var files_to_delete = []
+var dirs_to_delete = []
+
+// Gather packages to clean
+var packages_to_clean = []
+
+if (is_shop_scope) {
+  packages_to_clean = shop.list_packages()
+} else if (is_world_scope) {
+  // For now, world is the same as shop
+  packages_to_clean = shop.list_packages()
+} else {
+  // Single package
+  packages_to_clean.push(scope)
+
+  if (deep) {
+    try {
+      var deps = pkg.gather_dependencies(scope)
+      for (var dep of deps) {
+        packages_to_clean.push(dep)
+      }
+    } catch (e) {
+      // Skip if can't read dependencies
+    }
+  }
+}
+
+// Gather files to clean
+var lib_dir = shop.get_lib_dir()
+var build_dir = shop.get_build_dir()
+var packages_dir = shop.get_package_dir('').replace(/\/$/, '') // Get base packages dir
+
+if (clean_build) {
+  if (is_shop_scope) {
+    // Clean entire build and lib directories
+    if (fd.is_dir(build_dir)) {
+      dirs_to_delete.push(build_dir)
+    }
+    if (fd.is_dir(lib_dir)) {
+      dirs_to_delete.push(lib_dir)
+    }
+  } else {
+    // Clean specific package libraries
+    for (var p of packages_to_clean) {
+      if (p == 'core') continue
+
+      var lib_name = shop.lib_name_for_package(p)
+      var dylib_ext = '.dylib'
+      var lib_path = lib_dir + '/' + lib_name + dylib_ext
+
+      if (fd.is_file(lib_path)) {
+        files_to_delete.push(lib_path)
+      }
+
+      // Also check for .so and .dll
+      var so_path = lib_dir + '/' + lib_name + '.so'
+      var dll_path = lib_dir + '/' + lib_name + '.dll'
+      if (fd.is_file(so_path)) {
+        files_to_delete.push(so_path)
+      }
+      if (fd.is_file(dll_path)) {
+        files_to_delete.push(dll_path)
+      }
+    }
+  }
+}
+
+if (clean_fetch) {
+  if (is_shop_scope) {
+    // Clean entire packages directory (dangerous!)
+    if (fd.is_dir(packages_dir)) {
+      dirs_to_delete.push(packages_dir)
+    }
+  } else {
+    // Clean specific package directories
+    for (var p of packages_to_clean) {
+      if (p == 'core') continue
+
+      var pkg_dir = shop.get_package_dir(p)
+      if (fd.is_dir(pkg_dir) || fd.is_link(pkg_dir)) {
+        dirs_to_delete.push(pkg_dir)
+      }
+    }
+  }
+}
+
+// Execute or report
+if (dry_run) {
+  log.console("Would delete:")
+  if (files_to_delete.length == 0 && dirs_to_delete.length == 0) {
+    log.console("  (nothing to clean)")
+  } else {
+    for (var f of files_to_delete) {
+      log.console("  [file] " + f)
+    }
+    for (var d of dirs_to_delete) {
+      log.console("  [dir]  " + d)
+    }
+  }
+} else {
+  var deleted_count = 0
+
+  for (var f of files_to_delete) {
+    try {
+      fd.unlink(f)
+      log.console("Deleted: " + f)
+      deleted_count++
+    } catch (e) {
+      log.error("Failed to delete " + f + ": " + e)
+    }
+  }
+
+  for (var d of dirs_to_delete) {
+    try {
+      if (fd.is_link(d)) {
+        fd.unlink(d)
+      } else {
+        fd.rmdir(d, 1) // recursive
+      }
+      log.console("Deleted: " + d)
+      deleted_count++
+    } catch (e) {
+      log.error("Failed to delete " + d + ": " + e)
+    }
+  }
+
+  if (deleted_count == 0) {
+    log.console("Nothing to clean.")
+  } else {
+    log.console("")
+    log.console("Clean complete: " + text(deleted_count) + " item(s) deleted.")
+  }
+}
+
+$stop()

graph.ce

@@ -0,0 +1,236 @@
+// cell graph [<locator>] - Emit dependency graph
+//
+// Usage:
+//   cell graph             Graph current directory package
+//   cell graph .           Graph current directory package
+//   cell graph <locator>   Graph specific package
+//   cell graph --world     Graph all packages in shop (world set)
+//
+// Options:
+//   --format <fmt>   Output format: tree (default), dot, json
+//   --resolved       Show resolved view with links applied (default)
+//   --locked         Show lock view without links
+//   --world          Graph all packages in shop
+
+var shop = use('internal/shop')
+var pkg = use('package')
+var link = use('link')
+var fd = use('fd')
+var json = use('json')
+
+var target_locator = null
+var format = 'tree'
+var show_locked = false
+var show_world = false
+
+for (var i = 0; i < args.length; i++) {
+  if (args[i] == '--format' || args[i] == '-f') {
+    if (i + 1 < args.length) {
+      format = args[++i]
+      if (format != 'tree' && format != 'dot' && format != 'json') {
+        log.error('Invalid format: ' + format + '. Must be tree, dot, or json')
+        $stop()
+      }
+    } else {
+      log.error('--format requires a format type')
+      $stop()
+    }
+  } else if (args[i] == '--resolved') {
+    show_locked = false
+  } else if (args[i] == '--locked') {
+    show_locked = true
+  } else if (args[i] == '--world') {
+    show_world = true
+  } else if (args[i] == '--help' || args[i] == '-h') {
+    log.console("Usage: cell graph [<locator>] [options]")
+    log.console("")
+    log.console("Emit the dependency graph.")
+    log.console("")
+    log.console("Options:")
+    log.console("  --format <fmt>  Output format: tree (default), dot, json")
+    log.console("  --resolved      Show resolved view with links applied (default)")
+    log.console("  --locked        Show lock view without links")
+    log.console("  --world         Graph all packages in shop")
+    $stop()
+  } else if (!args[i].startsWith('-')) {
+    target_locator = args[i]
+  }
+}
+
+var links = show_locked ? {} : link.load()
+
+// Get effective locator (after links)
+function get_effective(locator) {
+  return links[locator] || locator
+}
+
+// Build graph data structure
+var nodes = {}
+var edges = []
+
+function add_node(locator) {
+  if (nodes[locator]) return
+
+  var lock = shop.load_lock()
+  var lock_entry = lock[locator]
+  var link_target = links[locator]
+  var info = shop.resolve_package_info(locator)
+
+  nodes[locator] = {
+    id: locator,
+    effective: get_effective(locator),
+    linked: link_target != null,
+    local: info == 'local',
+    commit: lock_entry && lock_entry.commit ? lock_entry.commit.substring(0, 8) : null
+  }
+}
+
+function gather_graph(locator, visited) {
+  if (visited[locator]) return
+  visited[locator] = true
+
+  add_node(locator)
+
+  try {
+    var deps = pkg.dependencies(locator)
+    if (deps) {
+      for (var alias in deps) {
+        var dep_locator = deps[alias]
+        add_node(dep_locator)
+        edges.push({ from: locator, to: dep_locator, alias: alias })
+        gather_graph(dep_locator, visited)
+      }
+    }
+  } catch (e) {
+    // Package might not have dependencies
+  }
+}
+
+// Gather graph from roots
+var roots = []
+
+if (show_world) {
+  // Use all packages in shop as roots
+  var packages = shop.list_packages()
+  for (var p of packages) {
+    if (p != 'core') {
+      roots.push(p)
+    }
+  }
+} else {
+  // Default to current directory
+  if (!target_locator) {
+    target_locator = '.'
+  }
+
+  // Resolve local paths
+  if (target_locator == '.' || target_locator.startsWith('./') || target_locator.startsWith('../') || fd.is_dir(target_locator)) {
+    var resolved = fd.realpath(target_locator)
+    if (resolved) {
+      target_locator = resolved
+    }
+  }
+
+  roots.push(target_locator)
+}
+
+for (var root of roots) {
+  gather_graph(root, {})
+}
+
+// Output based on format
+if (format == 'tree') {
+  function print_tree(locator, prefix, is_last, visited) {
+    if (visited[locator]) {
+      log.console(prefix + (is_last ? "\\-- " : "|-- ") + locator + " (circular)")
+      return
+    }
+    visited[locator] = true
+
+    var node = nodes[locator]
+    var suffix = ""
+    if (node.linked) suffix += " -> " + node.effective
+    if (node.commit) suffix += " @" + node.commit
+    if (node.local) suffix += " (local)"
+
+    log.console(prefix + (is_last ? "\\-- " : "|-- ") + locator + suffix)
+
+    // Get children
+    var children = []
+    for (var e of edges) {
+      if (e.from == locator) {
+        children.push(e)
+      }
+    }
+
+    for (var i = 0; i < children.length; i++) {
+      var child_prefix = prefix + (is_last ? "    " : "|   ")
+      print_tree(children[i].to, child_prefix, i == children.length - 1, visited)
+    }
+  }
+
+  for (var i = 0; i < roots.length; i++) {
+    log.console(roots[i])
+
+    var children = []
+    for (var e of edges) {
+      if (e.from == roots[i]) {
+        children.push(e)
+      }
+    }
+
+    for (var j = 0; j < children.length; j++) {
+      print_tree(children[j].to, "", j == children.length - 1, {})
+    }
+
+    if (i < roots.length - 1) log.console("")
+  }
+
+} else if (format == 'dot') {
+  log.console("digraph dependencies {")
+  log.console("  rankdir=TB;")
+  log.console("  node [shape=box];")
+  log.console("")
+
+  // Node definitions
+  for (var id in nodes) {
+    var node = nodes[id]
+    var label = id
+    if (node.commit) label += "\\n@" + node.commit
+    var attrs = 'label="' + label + '"'
+    if (node.linked) attrs += ', style=dashed'
+    if (node.local) attrs += ', color=blue'
+
+    // Safe node ID for dot
+    var safe_id = id.replaceAll(/[^a-zA-Z0-9]/g, '_')
+    log.console('  ' + safe_id + ' [' + attrs + '];')
+  }
+
+  log.console("")
+
+  // Edges
+  for (var e of edges) {
+    var from_id = e.from.replaceAll(/[^a-zA-Z0-9]/g, '_')
+    var to_id = e.to.replaceAll(/[^a-zA-Z0-9]/g, '_')
+    var label = e.alias != e.to ? 'label="' + e.alias + '"' : ''
+    log.console('  ' + from_id + ' -> ' + to_id + (label ? ' [' + label + ']' : '') + ';')
+  }
+
+  log.console("}")
+
+} else if (format == 'json') {
+  var output = {
+    nodes: [],
+    edges: []
+  }
+
+  for (var id in nodes) {
+    output.nodes.push(nodes[id])
+  }
+
+  output.edges = edges
+
+  log.console(json.encode(output))
+}
+
+$stop()

help.ce

@@ -27,21 +27,41 @@ if (stat && stat.isFile) {
   log.console(content)
 } else {
   // Fallback if man file doesn't exist
-  log.console("cell - The Cell module system for Prosperon")
+  log.console("cell - The Cell package manager")
   log.console("")
   log.console("Usage: cell <command> [arguments]")
   log.console("")
-  log.console("Commands:")
-  log.console("  init      Initialize a new Cell project")
-  log.console("  get       Fetch and add a module dependency")
-  log.console("  update    Update a dependency to a new version")
-  log.console("  vendor    Copy all dependencies locally")
-  log.console("  build     Compile all modules to bytecode")
-  log.console("  patch     Create a patch for a module")
-  log.console("  config    Manage system and actor configurations")
-  log.console("  help      Show this help message")
+  log.console("Package Management:")
+  log.console("  install <locator>   Install a package and its dependencies")
+  log.console("  update [locator]    Update packages from remote sources")
+  log.console("  remove <locator>    Remove a package from the shop")
+  log.console("  add <locator>       Add a dependency to current package")
   log.console("")
-  log.console("Run 'cell help <command>' for more information on a command.")
+  log.console("Building:")
+  log.console("  build [locator]     Build dynamic libraries for packages")
+  log.console("  clean [scope]       Remove build artifacts")
+  log.console("")
+  log.console("Linking (Local Development):")
+  log.console("  link <origin> <target>  Link a package to a local path")
+  log.console("  unlink <origin>         Remove a package link")
+  log.console("  clone <origin> <path>   Clone and link a package locally")
+  log.console("")
+  log.console("Information:")
+  log.console("  list [scope]        List packages and dependencies")
+  log.console("  ls [locator]        List modules and actors in a package")
+  log.console("  why <locator>       Show reverse dependencies")
+  log.console("  search <query>      Search for packages, modules, or actors")
+  log.console("")
+  log.console("Diagnostics:")
+  log.console("  resolve [locator]   Print fully resolved dependency closure")
+  log.console("  graph [locator]     Emit dependency graph (tree, dot, json)")
+  log.console("  verify [scope]      Verify integrity and consistency")
+  log.console("")
+  log.console("Other:")
+  log.console("  help [command]      Show help for a command")
+  log.console("  version             Show cell version")
+  log.console("")
+  log.console("Run 'cell <command> --help' for more information on a command.")
 }
 
-$stop()
+$stop()

install.ce

@@ -1,17 +1,65 @@
 // cell install <locator> - Install a package to the shop
-// Does not modify the current project's cell.toml
+//
+// Usage:
+//   cell install <locator>   Install a package and its dependencies
+//   cell install .           Install current directory package
+//
+// Options:
+//   --target <triple>   Build for target platform
+//   --refresh           Refresh floating refs before locking
+//   --dry-run           Show what would be installed
 
 var shop = use('internal/shop')
 var build = use('build')
+var pkg = use('package')
 var fd = use('fd')
 
 if (args.length < 1) {
-  log.console("Usage: cell install <locator>")
+  log.console("Usage: cell install <locator> [options]")
+  log.console("")
+  log.console("Options:")
+  log.console("  --target <triple>  Build for target platform")
+  log.console("  --refresh          Refresh floating refs before locking")
+  log.console("  --dry-run          Show what would be installed")
   $stop()
-  return
 }
 
-var locator = args[0]
+var locator = null
+var target_triple = null
+var refresh = false
+var dry_run = false
+
+for (var i = 0; i < args.length; i++) {
+  if (args[i] == '--target' || args[i] == '-t') {
+    if (i + 1 < args.length) {
+      target_triple = args[++i]
+    } else {
+      log.error('--target requires a triple')
+      $stop()
+    }
+  } else if (args[i] == '--refresh') {
+    refresh = true
+  } else if (args[i] == '--dry-run') {
+    dry_run = true
+  } else if (args[i] == '--help' || args[i] == '-h') {
+    log.console("Usage: cell install <locator> [options]")
+    log.console("")
+    log.console("Install a package and its dependencies to the shop.")
+    log.console("")
+    log.console("Options:")
+    log.console("  --target <triple>  Build for target platform")
+    log.console("  --refresh          Refresh floating refs before locking")
+    log.console("  --dry-run          Show what would be installed")
+    $stop()
+  } else if (!args[i].startsWith('-')) {
+    locator = args[i]
+  }
+}
+
+if (!locator) {
+  log.console("Usage: cell install <locator>")
+  $stop()
+}
 
 // Resolve relative paths to absolute paths
 // Local paths like '.' or '../foo' need to be converted to absolute paths
@@ -22,41 +70,86 @@ if (locator == '.' || locator.startsWith('./') || locator.startsWith('../') || f
   }
 }
 
+// Default target
+if (!target_triple) {
+  target_triple = build.detect_host_target()
+}
+
 log.console("Installing " + locator + "...")
 
-var pkg = use('package')
+// Gather all packages that will be installed
+var packages_to_install = []
+var visited = {}
 
-// Recursive install function that handles dependencies
-function install_package(pkg_locator, visited) {
+function gather_packages(pkg_locator) {
   if (visited[pkg_locator]) return
   visited[pkg_locator] = true
-  
-  // First, add to lock.toml
-  shop.update(pkg_locator)
-  
-  // Extract/symlink the package so we can read its cell.toml
-  shop.extract(pkg_locator)
-  
-  // Now get direct dependencies and install them first
+
+  packages_to_install.push(pkg_locator)
+
+  // Try to read dependencies
   try {
+    // For packages not yet extracted, we need to update and extract first to read deps
+    var lock = shop.load_lock()
+    if (!lock[pkg_locator]) {
+      if (!dry_run) {
+        shop.update(pkg_locator)
+        shop.extract(pkg_locator)
+      }
+    }
+
     var deps = pkg.dependencies(pkg_locator)
     if (deps) {
       for (var alias in deps) {
         var dep_locator = deps[alias]
-        log.console("Installing dependency " + dep_locator)
-        install_package(dep_locator, visited)
+        gather_packages(dep_locator)
       }
     }
   } catch (e) {
     // Package might not have dependencies or cell.toml issue
-    log.console("Warning: Could not read dependencies for " + pkg_locator + ": " + e.message)
+    if (!dry_run) {
+      log.console("Warning: Could not read dependencies for " + pkg_locator + ": " + e.message)
+    }
   }
-  
-  // Build the package after all dependencies are installed
-  build.build_package(pkg_locator)
 }
 
-install_package(locator, {})
-log.console("Installed " + locator)
+// Gather all packages
+gather_packages(locator)
+
+if (dry_run) {
+  log.console("Would install:")
+  for (var p of packages_to_install) {
+    var lock = shop.load_lock()
+    var exists = lock[p] != null
+    log.console("  " + p + (exists ? " (already installed)" : ""))
+  }
+  $stop()
+}
+
+// Install each package
+function install_package(pkg_locator) {
+  // Update lock entry
+  shop.update(pkg_locator)
+
+  // Extract/symlink the package
+  shop.extract(pkg_locator)
+
+  // Build scripts
+  shop.build_package_scripts(pkg_locator)
+
+  // Build C code
+  try {
+    build.build_dynamic(pkg_locator, target_triple, 'release')
+  } catch (e) {
+    // Not all packages have C code
+  }
+}
+
+for (var p of packages_to_install) {
+  log.console("  Installing " + p + "...")
+  install_package(p)
+}
+
+log.console("Installed " + text(packages_to_install.length) + " package(s).")
 
 $stop()

internal/shop.cm

@@ -986,8 +986,15 @@ Shop.update = function(pkg) {
 
   log.console(`checking ${pkg}`)
 
-  if (info == 'local') return {
-    updated: time.number()
+  if (info == 'local') {
+    // Local packages always get a lock entry
+    var new_entry = {
+      type: 'local',
+      updated: time.number()
+    }
+    lock[pkg] = new_entry
+    Shop.save_lock(lock)
+    return new_entry
   }
   
   var local_commit = lock_entry ? lock_entry.commit : null

list.ce

@@ -1,85 +1,170 @@
-// list installed packages
-// cell list -> list packages installed in this package
-// cell list all -> list all packages (including those that are there due to installed packages)
-// cell list package <name> -> list the packages for the package <name>
+// cell list [<scope>] - List packages and dependencies
+//
+// Usage:
+//   cell list              List dependencies of current package
+//   cell list shop         List all packages in shop with status
+//   cell list <locator>    List dependency tree for a package
 
 var shop = use('internal/shop')
 var pkg = use('package')
+var link = use('link')
+var fd = use('fd')
 
 var mode = 'local'
 var target_pkg = null
 
 if (args && args.length > 0) {
-    if (args[0] == 'all') {
-        mode = 'all'
-    } else if (args[0] == 'shop') {
-        mode = 'shop'
-    } else if (args[0] == 'package') {
-        if (args.length < 2) {
-            log.console("Usage: cell list package <name>")
-            $stop()
-            return
-        }
-        mode = 'package'
-        target_pkg = args[1]
-    } else {
-        log.console("Usage:")
-        log.console("  cell list             : list local packages")
-        log.console("  cell list all         : list all recursive packages")
-        log.console("  cell list package <name>: list dependencies of <name>")
-        log.console("  cell list shop        : list all packages in shop")
-        $stop()
-        return
+  if (args[0] == 'shop') {
+    mode = 'shop'
+  } else if (args[0] == '--help' || args[0] == '-h') {
+    log.console("Usage: cell list [<scope>]")
+    log.console("")
+    log.console("List packages and dependencies.")
+    log.console("")
+    log.console("Scopes:")
+    log.console("  (none)     List dependencies of current package")
+    log.console("  shop       List all packages in shop with status")
+    log.console("  <locator>  List dependency tree for a package")
+    $stop()
+  } else {
+    mode = 'package'
+    target_pkg = args[0]
+
+    // Resolve local paths
+    if (target_pkg == '.' || target_pkg.startsWith('./') || target_pkg.startsWith('../') || fd.is_dir(target_pkg)) {
+      var resolved = fd.realpath(target_pkg)
+      if (resolved) {
+        target_pkg = resolved
+      }
     }
+  }
+}
+
+var links = link.load()
+var lock = shop.load_lock()
+
+function print_deps(ctx, indent) {
+  indent = indent || ""
+  var deps
+  try {
+    deps = pkg.dependencies(ctx)
+  } catch (e) {
+    log.console(indent + "  (could not read dependencies)")
+    return
+  }
+
+  if (!deps) {
+    log.console(indent + "  (none)")
+    return
+  }
+
+  var aliases = []
+  for (var k in deps) aliases.push(k)
+  aliases.sort()
+
+  if (aliases.length == 0) {
+    log.console(indent + "  (none)")
+    return
+  }
+
+  for (var i = 0; i < aliases.length; i++) {
+    var alias = aliases[i]
+    var locator = deps[alias]
+    var link_target = links[locator]
+    var lock_entry = lock[locator]
+
+    var line = indent + "  " + alias
+    if (alias != locator) {
+      line += " -> " + locator
+    }
+
+    // Add status indicators
+    var status = []
+    if (link_target) {
+      status.push("linked -> " + link_target)
+    }
+    if (lock_entry && lock_entry.commit) {
+      status.push("@" + lock_entry.commit.substring(0, 8))
+    }
+    if (lock_entry && lock_entry.type == 'local') {
+      status.push("local")
+    }
+    if (!lock_entry) {
+      status.push("not installed")
+    }
+
+    if (status.length > 0) {
+      line += " [" + status.join(", ") + "]"
+    }
+
+    log.console(line)
+  }
 }
 
 if (mode == 'local') {
-    log.console("Installed Packages (Local):")
-    print_deps(null)
+  log.console("Dependencies:")
+  print_deps(null)
 } else if (mode == 'package') {
-    // Resolve alias to canonical package path
-    var canon = shop.get_canonical_package(target_pkg, null)
-    if (!canon) {
-        log.console("Package '" + target_pkg + "' not found in local dependencies.")
-    } else {
-        log.console("Dependencies for " + target_pkg + " (" + canon + "):")
-        print_deps(canon)
-    }
-} else if (mode == 'all') {
-    log.console("All Packages:")
-    var all = shop.list_packages(null)
-    // list_packages returns an array of package strings (locators)
-    // We want to perhaps sort them
-    all.sort()
-    for (var i = 0; i < all.length; i++) {
-        log.console("  " + all[i])
-    }
-    if (all.length == 0) log.console("  (none)")
+  log.console("Dependencies for " + target_pkg + ":")
+  print_deps(target_pkg)
 } else if (mode == 'shop') {
-    log.console("Shop Packages:")
-    var all = shop.list_packages()
-    
-    if (all.length == 0)
-        log.console("  (none)")
-    else
-        all.forEach(package => log.console("  " + package))
-}
+  log.console("Shop packages:")
+  log.console("")
 
-function print_deps(ctx) {
-    var deps = pkg.dependencies(ctx)
-    var aliases = []
-    for (var k in deps) aliases.push(k)
-    aliases.sort()
+  var packages = shop.list_packages()
+  if (packages.length == 0) {
+    log.console("  (none)")
+  } else {
+    packages.sort()
 
-    if (aliases.length == 0) {
-        log.console("  (none)")
-    } else {
-        for (var i = 0; i < aliases.length; i++) {
-            var alias = aliases[i]
-            var locator = deps[alias]
-            log.console("  " + alias + " -> " + locator)
-        }
+    // Group by type
+    var local_pkgs = []
+    var linked_pkgs = []
+    var remote_pkgs = []
+
+    for (var p of packages) {
+      if (p == 'core') continue
+      var lock_entry = lock[p]
+      var link_target = links[p]
+
+      if (link_target) {
+        linked_pkgs.push(p)
+      } else if (lock_entry && lock_entry.type == 'local') {
+        local_pkgs.push(p)
+      } else {
+        remote_pkgs.push(p)
+      }
     }
+
+    if (linked_pkgs.length > 0) {
+      log.console("Linked packages:")
+      for (var p of linked_pkgs) {
+        var target = links[p]
+        log.console("  " + p + " -> " + target)
+      }
+      log.console("")
+    }
+
+    if (local_pkgs.length > 0) {
+      log.console("Local packages:")
+      for (var p of local_pkgs) {
+        log.console("  " + p)
+      }
+      log.console("")
+    }
+
+    if (remote_pkgs.length > 0) {
+      log.console("Remote packages:")
+      for (var p of remote_pkgs) {
+        var lock_entry = lock[p]
+        var commit = lock_entry && lock_entry.commit ? " @" + lock_entry.commit.substring(0, 8) : ""
+        log.console("  " + p + commit)
+      }
+      log.console("")
+    }
+
+    log.console("Total: " + text(packages.length) + " package(s)")
+  }
 }
 
 $stop()

remove.ce

@@ -1,24 +1,105 @@
-// cell remove <alias|path> - Remove a package from dependencies or shop
+// cell remove <locator> - Remove a package from the shop
+//
+// Usage:
+//   cell remove <locator>   Remove a package from the shop
+//   cell remove .           Remove current directory package from shop
+//
+// Options:
+//   --prune     Also remove packages no longer needed by any root
+//   --dry-run   Show what would be removed
 
 var shop = use('internal/shop')
+var pkg = use('package')
+var link = use('link')
 var fd = use('fd')
 
-if (args.length < 1) {
-  log.console("Usage: cell remove <alias|path>")
-  $stop()
-  return
-}
+var target_pkg = null
+var prune = false
+var dry_run = false
 
-var pkg = args[0]
-
-// Resolve relative paths to absolute paths
-if (pkg == '.' || pkg.startsWith('./') || pkg.startsWith('../') || fd.is_dir(pkg)) {
-  var resolved = fd.realpath(pkg)
-  if (resolved) {
-    pkg = resolved
+for (var i = 0; i < args.length; i++) {
+  if (args[i] == '--prune') {
+    prune = true
+  } else if (args[i] == '--dry-run') {
+    dry_run = true
+  } else if (args[i] == '--help' || args[i] == '-h') {
+    log.console("Usage: cell remove <locator> [options]")
+    log.console("")
+    log.console("Remove a package from the shop.")
+    log.console("")
+    log.console("Options:")
+    log.console("  --prune    Also remove packages no longer needed by any root")
+    log.console("  --dry-run  Show what would be removed")
+    $stop()
+  } else if (!args[i].startsWith('-')) {
+    target_pkg = args[i]
   }
 }
 
-shop.remove(pkg)
+if (!target_pkg) {
+  log.console("Usage: cell remove <locator> [options]")
+  $stop()
+}
+
+// Resolve relative paths to absolute paths
+if (target_pkg == '.' || target_pkg.startsWith('./') || target_pkg.startsWith('../') || fd.is_dir(target_pkg)) {
+  var resolved = fd.realpath(target_pkg)
+  if (resolved) {
+    target_pkg = resolved
+  }
+}
+
+var packages_to_remove = [target_pkg]
+
+if (prune) {
+  // Find packages no longer needed
+  // Get all dependencies of remaining packages
+  var lock = shop.load_lock()
+  var all_packages = shop.list_packages()
+
+  // Build set of all needed packages (excluding target)
+  var needed = {}
+  for (var p of all_packages) {
+    if (p == target_pkg || p == 'core') continue
+
+    // Mark this package and its deps as needed
+    needed[p] = true
+    try {
+      var deps = pkg.gather_dependencies(p)
+      for (var dep of deps) {
+        needed[dep] = true
+      }
+    } catch (e) {
+      // Skip if can't read deps
+    }
+  }
+
+  // Find packages that are NOT needed
+  for (var p of all_packages) {
+    if (p == 'core') continue
+    if (!needed[p] && packages_to_remove.indexOf(p) < 0) {
+      packages_to_remove.push(p)
+    }
+  }
+}
+
+if (dry_run) {
+  log.console("Would remove:")
+  for (var p of packages_to_remove) {
+    log.console("  " + p)
+  }
+} else {
+  for (var p of packages_to_remove) {
+    // Remove any link for this package
+    if (link.is_linked(p)) {
+      link.remove(p)
+    }
+
+    // Remove from shop
+    shop.remove(p)
+  }
+
+  log.console("Removed " + text(packages_to_remove.length) + " package(s).")
+}
 
 $stop()

resolve.ce

@@ -0,0 +1,201 @@
+// cell resolve [<locator>] - Print fully resolved dependency closure
+//
+// Usage:
+//   cell resolve           Resolve current directory package
+//   cell resolve .         Resolve current directory package
+//   cell resolve <locator> Resolve specific package
+//
+// Options:
+//   --target <triple>      Annotate builds for target platform
+//   --locked               Show lock state without applying links
+//   --refresh              Refresh floating refs before printing
+
+var shop = use('internal/shop')
+var pkg = use('package')
+var link = use('link')
+var build = use('build')
+var fd = use('fd')
+
+var target_locator = null
+var target_triple = null
+var show_locked = false
+var refresh_first = false
+
+for (var i = 0; i < args.length; i++) {
+  if (args[i] == '--target' || args[i] == '-t') {
+    if (i + 1 < args.length) {
+      target_triple = args[++i]
+    } else {
+      log.error('--target requires a triple')
+      $stop()
+    }
+  } else if (args[i] == '--locked') {
+    show_locked = true
+  } else if (args[i] == '--refresh') {
+    refresh_first = true
+  } else if (args[i] == '--help' || args[i] == '-h') {
+    log.console("Usage: cell resolve [<locator>] [options]")
+    log.console("")
+    log.console("Print the fully resolved dependency closure.")
+    log.console("")
+    log.console("Options:")
+    log.console("  --target <triple>  Annotate builds for target platform")
+    log.console("  --locked           Show lock state without applying links")
+    log.console("  --refresh          Refresh floating refs before printing")
+    $stop()
+  } else if (!args[i].startsWith('-')) {
+    target_locator = args[i]
+  }
+}
+
+// Default to current directory
+if (!target_locator) {
+  target_locator = '.'
+}
+
+// Resolve local paths
+if (target_locator == '.' || target_locator.startsWith('./') || target_locator.startsWith('../') || fd.is_dir(target_locator)) {
+  var resolved = fd.realpath(target_locator)
+  if (resolved) {
+    target_locator = resolved
+  }
+}
+
+// Check if it's a valid package
+if (!fd.is_file(target_locator + '/cell.toml')) {
+  // Try to find it in the shop
+  var pkg_dir = shop.get_package_dir(target_locator)
+  if (!fd.is_file(pkg_dir + '/cell.toml')) {
+    log.error("Not a valid package: " + target_locator)
+    $stop()
+  }
+}
+
+// Detect target if not specified
+if (!target_triple) {
+  target_triple = build.detect_host_target()
+}
+
+var lock = shop.load_lock()
+var links = link.load()
+
+// Gather all dependencies recursively
+var all_deps = {}
+var visited = {}
+
+function gather_deps(locator, depth) {
+  if (visited[locator]) return
+  visited[locator] = true
+
+  all_deps[locator] = { depth: depth }
+
+  try {
+    var deps = pkg.dependencies(locator)
+    if (deps) {
+      for (var alias in deps) {
+        var dep_locator = deps[alias]
+        gather_deps(dep_locator, depth + 1)
+      }
+    }
+  } catch (e) {
+    // Package might not have dependencies
+  }
+}
+
+gather_deps(target_locator, 0)
+
+// Print header
+log.console("Resolved dependency closure for: " + target_locator)
+log.console("Target: " + target_triple)
+log.console("")
+
+// Sort by depth then alphabetically
+var sorted = []
+for (var locator in all_deps) {
+  sorted.push({ locator: locator, depth: all_deps[locator].depth })
+}
+sorted.sort(function(a, b) {
+  if (a.depth != b.depth) return a.depth - b.depth
+  return a.locator < b.locator ? -1 : 1
+})
+
+for (var i = 0; i < sorted.length; i++) {
+  var locator = sorted[i].locator
+  var depth = sorted[i].depth
+
+  var indent = ""
+  for (var j = 0; j < depth; j++) indent += "  "
+
+  // Get info about this package
+  var info = shop.resolve_package_info(locator)
+  var lock_entry = lock[locator]
+  var link_target = show_locked ? null : links[locator]
+  var effective_locator = link_target || locator
+
+  // Check status
+  var is_linked = link_target != null
+  var is_in_lock = lock_entry != null
+  var is_local = info == 'local'
+
+  // Check if fetched (package directory exists)
+  var pkg_dir = shop.get_package_dir(locator)
+  var is_fetched = fd.is_dir(pkg_dir) || fd.is_link(pkg_dir)
+
+  // Check if built (library exists)
+  var lib_dir = shop.get_lib_dir()
+  var lib_name = shop.lib_name_for_package(locator)
+  var dylib_ext = '.dylib' // TODO: detect from target
+  var lib_path = lib_dir + '/' + lib_name + dylib_ext
+  var is_built = fd.is_file(lib_path)
+
+  // Format output
+  var status_parts = []
+  if (is_linked) status_parts.push("linked")
+  if (is_local) status_parts.push("local")
+  if (!is_in_lock) status_parts.push("not in lock")
+  if (!is_fetched) status_parts.push("not fetched")
+  if (is_built) status_parts.push("built")
+
+  var commit_str = ""
+  if (lock_entry && lock_entry.commit) {
+    commit_str = " @" + lock_entry.commit.substring(0, 8)
+  } else if (lock_entry && lock_entry.type == 'local') {
+    commit_str = " (local)"
+  }
+
+  var line = indent + locator + commit_str
+
+  if (is_linked && !show_locked) {
+    line += " -> " + link_target
+  }
+
+  if (status_parts.length > 0) {
+    line += " [" + status_parts.join(", ") + "]"
+  }
+
+  log.console(line)
+
+  // Show compilation inputs if requested (verbose)
+  if (depth == 0) {
+    try {
+      var cflags = pkg.get_flags(locator, 'CFLAGS', target_triple)
+      var ldflags = pkg.get_flags(locator, 'LDFLAGS', target_triple)
+      if (cflags.length > 0 || ldflags.length > 0) {
+        log.console(indent + "  Compilation inputs:")
+        if (cflags.length > 0) {
+          log.console(indent + "    CFLAGS: " + cflags.join(' '))
+        }
+        if (ldflags.length > 0) {
+          log.console(indent + "    LDFLAGS: " + ldflags.join(' '))
+        }
+      }
+    } catch (e) {
+      // Skip if can't read config
+    }
+  }
+}
+
+log.console("")
+log.console("Total: " + text(sorted.length) + " package(s)")
+
+$stop()

update.ce

@@ -1,30 +1,47 @@
-// cell update - Update packages from remote sources
-//
-// This command checks for updates to all packages and downloads new versions.
-// For local packages, ensures the symlink is correct.
-// For remote packages, checks the remote for new commits.
+// cell update [<locator>] - Update packages from remote sources
 //
 // Usage:
-//   cell update           - Update all packages
-//   cell update <package> - Update a specific package
+//   cell update              Update all packages in shop
+//   cell update .            Update current directory package
+//   cell update <locator>    Update a specific package
+//
+// Options:
+//   --build              Run build after updating
+//   --target <triple>    Target platform for build (requires --build)
+//   --follow-links       Update link targets instead of origins
 
 var shop = use('internal/shop')
+var build = use('build')
 var fd = use('fd')
 
 var target_pkg = null
+var run_build = false
+var target_triple = null
+var follow_links = false
 
 // Parse arguments
 for (var i = 0; i < args.length; i++) {
   if (args[i] == '--help' || args[i] == '-h') {
-    log.console("Usage: cell update [package]")
+    log.console("Usage: cell update [<locator>] [options]")
+    log.console("")
     log.console("Update packages from remote sources.")
     log.console("")
-    log.console("Arguments:")
-    log.console("  package  Optional package name to update. If omitted, updates all.")
-    log.console("")
-    log.console("This command checks for updates to all packages and downloads")
-    log.console("new versions. For local packages, ensures the symlink is correct.")
+    log.console("Options:")
+    log.console("  --build              Run build after updating")
+    log.console("  --target <triple>    Target platform for build (requires --build)")
+    log.console("  --follow-links       Update link targets instead of origins")
     $stop()
+  } else if (args[i] == '--build') {
+    run_build = true
+  } else if (args[i] == '--target' || args[i] == '-t') {
+    if (i + 1 < args.length) {
+      target_triple = args[++i]
+    } else {
+      log.error('--target requires a triple')
+      $stop()
+    }
+  } else if (args[i] == '--follow-links') {
+    follow_links = true
   } else if (!args[i].startsWith('-')) {
     target_pkg = args[i]
     // Resolve relative paths to absolute paths
@@ -37,56 +54,94 @@ for (var i = 0; i < args.length; i++) {
   }
 }
 
+// Default target if building
+if (run_build && !target_triple) {
+  target_triple = build.detect_host_target()
+}
+
+var link = use('link')
+
 function update_and_fetch(pkg)
 {
   var lock = shop.load_lock()
   var old_entry = lock[pkg]
   var old_commit = old_entry ? old_entry.commit : null
-  
-  var new_entry = shop.update(pkg)
-  
+
+  // Handle follow-links option
+  var effective_pkg = pkg
+  if (follow_links) {
+    var link_target = link.get_target(pkg)
+    if (link_target) {
+      effective_pkg = link_target
+      log.console("  Following link: " + pkg + " -> " + effective_pkg)
+    }
+  }
+
+  var new_entry = shop.update(effective_pkg)
+
   if (new_entry) {
     if (new_entry.commit) {
       var old_str = old_commit ? old_commit.substring(0, 8) : "(new)"
-      log.console("  " + pkg + " " + old_str + " -> " + new_entry.commit.substring(0, 8))
-      shop.fetch(pkg)
+      log.console("  " + effective_pkg + " " + old_str + " -> " + new_entry.commit.substring(0, 8))
+      shop.fetch(effective_pkg)
     } else {
       // Local package - just ensure symlink is correct
-      log.console("  " + pkg + " (local)")
+      log.console("  " + effective_pkg + " (local)")
     }
-    shop.extract(pkg)
-    shop.build_package_scripts(pkg)
-    return true
+    shop.extract(effective_pkg)
+    shop.build_package_scripts(effective_pkg)
+    return effective_pkg
   }
-  return false
+  return null
 }
 
+var updated_packages = []
+
 if (target_pkg) {
-  if (update_and_fetch(target_pkg))
+  var updated = update_and_fetch(target_pkg)
+  if (updated) {
+    updated_packages.push(updated)
     log.console("Updated " + target_pkg + ".")
-  else
+  } else {
     log.console(target_pkg + " is up to date.")
+  }
 } else {
   var packages = shop.list_packages()
   var pkg_count = packages.length
   log.console("Checking for updates (" + text(pkg_count) + " package" + (pkg_count == 1 ? "" : "s") + ")...")
-  
-  var updated_count = 0
-  
+
   for (var i = 0; i < packages.length; i++) {
     var pkg = packages[i]
     if (pkg == 'core') continue
-    
-    if (update_and_fetch(pkg)) {
-      updated_count++
+
+    var updated = update_and_fetch(pkg)
+    if (updated) {
+      updated_packages.push(updated)
     }
   }
-  
-  if (updated_count > 0) {
-    log.console("Updated " + text(updated_count) + " package" + (updated_count == 1 ? "" : "s") + ".")
+
+  if (updated_packages.length > 0) {
+    log.console("Updated " + text(updated_packages.length) + " package" + (updated_packages.length == 1 ? "" : "s") + ".")
   } else {
     log.console("All packages are up to date.")
   }
 }
 
+// Run build if requested
+if (run_build && updated_packages.length > 0) {
+  log.console("")
+  log.console("Building updated packages...")
+
+  for (var pkg of updated_packages) {
+    try {
+      var lib = build.build_dynamic(pkg, target_triple, 'release')
+      if (lib) {
+        log.console("  Built: " + lib)
+      }
+    } catch (e) {
+      log.error("  Failed to build " + pkg + ": " + e)
+    }
+  }
+}
+
 $stop()

verify.ce

@@ -0,0 +1,257 @@
+// cell verify [<scope>] - Verify integrity and consistency
+//
+// Usage:
+//   cell verify             Verify current directory package
+//   cell verify .           Verify current directory package
+//   cell verify <locator>   Verify specific package
+//   cell verify shop        Verify entire shop
+//   cell verify world       Verify all world roots
+//
+// Options:
+//   --deep                  Traverse full dependency closure
+//   --target <triple>       Verify builds for specific target
+
+var shop = use('internal/shop')
+var pkg = use('package')
+var link = use('link')
+var build = use('build')
+var fd = use('fd')
+
+var scope = null
+var deep = false
+var target_triple = null
+
+for (var i = 0; i < args.length; i++) {
+  if (args[i] == '--deep') {
+    deep = true
+  } else if (args[i] == '--target' || args[i] == '-t') {
+    if (i + 1 < args.length) {
+      target_triple = args[++i]
+    } else {
+      log.error('--target requires a triple')
+      $stop()
+    }
+  } else if (args[i] == '--help' || args[i] == '-h') {
+    log.console("Usage: cell verify [<scope>] [options]")
+    log.console("")
+    log.console("Verify integrity and consistency.")
+    log.console("")
+    log.console("Scopes:")
+    log.console("  <locator>  Verify specific package")
+    log.console("  shop       Verify entire shop")
+    log.console("  world      Verify all world roots")
+    log.console("")
+    log.console("Options:")
+    log.console("  --deep             Traverse full dependency closure")
+    log.console("  --target <triple>  Verify builds for specific target")
+    $stop()
+  } else if (!args[i].startsWith('-')) {
+    scope = args[i]
+  }
+}
+
+// Default to current directory
+if (!scope) {
+  scope = '.'
+}
+
+// Detect target if not specified
+if (!target_triple) {
+  target_triple = build.detect_host_target()
+}
+
+var errors = []
+var warnings = []
+var checked = 0
+
+function add_error(msg) {
+  errors.push(msg)
+}
+
+function add_warning(msg) {
+  warnings.push(msg)
+}
+
+// Verify a single package
+function verify_package(locator) {
+  checked++
+
+  var lock = shop.load_lock()
+  var lock_entry = lock[locator]
+  var links = link.load()
+  var link_target = links[locator]
+
+  // Check lock entry exists
+  if (!lock_entry) {
+    add_error(locator + ": not in lock")
+  }
+
+  // Check package directory exists
+  var pkg_dir = shop.get_package_dir(locator)
+  var dir_exists = fd.is_dir(pkg_dir) || fd.is_link(pkg_dir)
+
+  if (!dir_exists) {
+    add_error(locator + ": package directory missing at " + pkg_dir)
+    return
+  }
+
+  // Check cell.toml exists
+  if (!fd.is_file(pkg_dir + '/cell.toml')) {
+    add_error(locator + ": missing cell.toml")
+    return
+  }
+
+  // For linked packages, verify link target
+  if (link_target) {
+    if (link_target.startsWith('/')) {
+      // Local path target
+      if (!fd.is_dir(link_target)) {
+        add_error(locator + ": link target does not exist: " + link_target)
+      } else if (!fd.is_file(link_target + '/cell.toml')) {
+        add_error(locator + ": link target is not a valid package: " + link_target)
+      }
+    } else {
+      // Package target
+      var target_dir = shop.get_package_dir(link_target)
+      if (!fd.is_dir(target_dir) && !fd.is_link(target_dir)) {
+        add_error(locator + ": link target package not found: " + link_target)
+      }
+    }
+
+    // Check symlink is correct
+    if (fd.is_link(pkg_dir)) {
+      var current_target = fd.readlink(pkg_dir)
+      var expected_target = link_target.startsWith('/') ? link_target : shop.get_package_dir(link_target)
+      if (current_target != expected_target) {
+        add_warning(locator + ": symlink target mismatch (expected " + expected_target + ", got " + current_target + ")")
+      }
+    } else {
+      add_warning(locator + ": linked but directory is not a symlink")
+    }
+  }
+
+  // Check build output exists
+  var lib_dir = shop.get_lib_dir()
+  var lib_name = shop.lib_name_for_package(locator)
+  var dylib_ext = '.dylib' // TODO: detect from target
+  var lib_path = lib_dir + '/' + lib_name + dylib_ext
+
+  // Only check for builds if package has C files
+  try {
+    var c_files = pkg.get_c_files(locator, target_triple, true)
+    if (c_files && c_files.length > 0) {
+      if (!fd.is_file(lib_path)) {
+        add_warning(locator + ": library not built at " + lib_path)
+      }
+    }
+  } catch (e) {
+    // Skip build check if can't determine C files
+  }
+}
+
+// Check for link cycles
+function check_link_cycles() {
+  var links = link.load()
+
+  function follow_chain(origin, visited) {
+    if (visited[origin]) {
+      return origin // cycle detected
+    }
+    visited[origin] = true
+
+    var target = links[origin]
+    if (target && links[target]) {
+      return follow_chain(target, visited)
+    }
+    return null
+  }
+
+  for (var origin in links) {
+    var cycle_start = follow_chain(origin, {})
+    if (cycle_start) {
+      add_error("Link cycle detected starting from: " + origin)
+    }
+  }
+}
+
+// Check for dangling links
+function check_dangling_links() {
+  var links = link.load()
+
+  for (var origin in links) {
+    var target = links[origin]
+    if (target.startsWith('/')) {
+      if (!fd.is_dir(target)) {
+        add_error("Dangling link: " + origin + " -> " + target + " (target does not exist)")
+      }
+    }
+  }
+}
+
+// Gather packages to verify
+var packages_to_verify = []
+
+if (scope == 'shop') {
+  packages_to_verify = shop.list_packages()
+} else if (scope == 'world') {
+  // For now, world is the same as shop
+  // In future, this could be a separate concept
+  packages_to_verify = shop.list_packages()
+} else {
+  // Single package
+  var locator = scope
+
+  // Resolve local paths
+  if (locator == '.' || locator.startsWith('./') || locator.startsWith('../') || fd.is_dir(locator)) {
+    var resolved = fd.realpath(locator)
+    if (resolved) {
+      locator = resolved
+    }
+  }
+
+  if (deep) {
+    // Gather all dependencies
+    var all_deps = pkg.gather_dependencies(locator)
+    packages_to_verify.push(locator)
+    for (var dep of all_deps) {
+      packages_to_verify.push(dep)
+    }
+  } else {
+    packages_to_verify.push(locator)
+  }
+}
+
+log.console("Verifying " + text(packages_to_verify.length) + " package(s)...")
+log.console("")
+
+// Run verification
+check_link_cycles()
+check_dangling_links()
+
+for (var p of packages_to_verify) {
+  if (p == 'core') continue
+  verify_package(p)
+}
+
+// Print results
+if (warnings.length > 0) {
+  log.console("Warnings:")
+  for (var w of warnings) {
+    log.console("  " + w)
+  }
+  log.console("")
+}
+
+if (errors.length > 0) {
+  log.console("Errors:")
+  for (var e of errors) {
+    log.console("  " + e)
+  }
+  log.console("")
+  log.console("Verification FAILED: " + text(errors.length) + " error(s), " + text(warnings.length) + " warning(s)")
+  // Note: would use process.exit(1) if available
+} else {
+  log.console("Verification PASSED: " + text(checked) + " package(s) checked, " + text(warnings.length) + " warning(s)")
+}
+
+$stop()