This rspec doesn't help too much in debugging what's going wrong in Palco::Base. There are too few stories with too much matchers contained. Let's use KISS to break it down.

palco.rb

# Public: the base palco skelethon builder.
#
# Ideally it will never called directly but it will be subclassed by
# Palco::Extension and Palco::Application
#
# Examples:
#
#   base = Palco::Base.new('a_test', [{:name=>'README', :file=>true}, {:name=>'lib', :file=>false}])
#   base.generate
#
module Palco
  class Base

    # Public: creates a new base palco instance. 
    #
    # The idea is that specialized classes extending Palco::Base will be aware
    # about the list of files and directories to be created, meanwhile the
    # Palco::Base takes this list without any clue about their meaning.
    # 
    # name - the name of the Sinatra project
    # items_list - an array containing a list of hashes with name of the file to
    #   be created and a second param telling the code code it the item is either
    #   a file or a directory.
    # 
    # Example
    #
    #   base = Palco::Base.new('test_one',[{:name=>'README', :file=>true}, {:name=>'lib', :file=>false}]) 
    # Returns
    #   A new Palco::Base object 

    attr_reader :project_name
    attr_reader :items_list
    attr_reader :valid
    attr_reader :generated

    def initialize(name=nil, items_list=[])
      @project_name = name
      @items_list = items_list
      @generated = false

      if @project_name.nil? or @items_list.size==0
        @valid = false
      else
        @valid = true
      end
    end
    
    # Public: generates the skelethon
    #
    # Example
    #   base = Palco::Base.new('test_one',[{:name=>'README', :file=>true}, {:name=>'lib', :file=>false}]) 
    #   base.generate
    #
    # Returns
    #   True if every item in the item list has been created of false otherwise.
    #
    def generate
      begin
        root_dir = Dir.mkdir(@project_name, 0700)
        Dir.chdir(@project_name)
        @items_list.each do |item|
          f= item[:file]
          if f
            File.touch(File.join(@project_name), item[:name])
          else
            Dir.mkdir(item[:name])
          end
        end
        @generated = true
        return true
      rescue SystemCallError
        return false
      end

    end

    # Public: destroy the skelethon removing all files and all directories.
    #   Also the base directory has been removed as well.
    #
    # Please note that you're not supposed to call destroy for a non generated
    # skelethon. The method returns false in this case.
    #
    # Example
    #   base = Palco::Base.new('test_one',[{:name=>'README', :file=>true}, {:name=>'lib', :file=>false}]) 
    #   base.generate
    #   base.destroy
    # 
    # Returns
    #   True if all items in the item list has been removed or false otherwise.
    #   
    def destroy
      true
    end

    def valid?
      return self.valid
    end

    def generate?
      return self.generate
    end

  end
end

palco_base_helper.rb

require 'spec_helper'

describe "Palco::Base package " do
  
  before(:all) do
    @base = Palco::Base.new('test_one', [{:name=>'README', :file=>true}, {:name=>'a_directory', :file=>false}])
  end

  it "creates a project named 'test_one'" do
    @base.project_name.should == "test_one"
    @base.valid?.should be_true
    @base.generate.should be_true
    File.directory?("test_one").should be_true
  end

  it "creates a README file in 'test_one' directory" do
    File.exists?("test_one/README").should be_true
  end

  it "creates a directory called 'a_directory' inside 'test_one'" do
    File.directory?("test_one/a_directory").should be_true
  end

  it "removes all if destroy method has been called" do
    @base.destroy
    @base.valid?.should be_false
    File.directory?("test_one").should be_false
    File.exists?("test_one/README").should be_false
    File.directory?("test_one/a_directory").should be_false
  end

  it "cannot remove a skelethon that it has not been generated before" do
    @base = Palco::Base.new('test_two', [{:name=>'README', :file=>true}, {:name=>'a_directory', :file=>false}])
    File.directory?("test_one").should be_false
    File.exists?("test_one/README").should be_false
    File.directory?("test_one/a_directory").should be_false
    @base.destroy.should be_false
  end

  it "must provide an handy generated? handler telling that everything is ok" do
    @base = Palco::Base.new('test_three', [{:name=>'README', :file=>true}, {:name=>'a_directory', :file=>false}])
    @base.generated?.should be_false
    @base.generate
    File.directory?("test_one").should be_true
    File.exists?("test_one/README").should be_true
    File.directory?("test_one/a_directory").should be_true
    @base.generated?.should be_true


  end
end