diff --git a/src/Dependency.cpp b/src/Dependency.cpp
index c51e4fe..c5c23aa 100644
--- a/src/Dependency.cpp
+++ b/src/Dependency.cpp
@@ -21,43 +21,6 @@
 #include "Settings.h"
 #include "Utils.h"
 
-// the paths to search for dylibs, store it globally to parse the environment variables only once
-std::vector<std::string> paths;
-
-// initialize the dylib search paths
-void initSearchPaths()
-{
-    // check the same paths the system would search for dylibs
-    std::string searchPaths;
-    char *dyldLibPath = std::getenv("DYLD_LIBRARY_PATH");
-    if (dyldLibPath != 0)
-        searchPaths = dyldLibPath;
-    dyldLibPath = std::getenv("DYLD_FALLBACK_FRAMEWORK_PATH");
-    if (dyldLibPath != 0) {
-        if (!searchPaths.empty() && searchPaths[searchPaths.size()-1] != ':')
-            searchPaths += ":";
-        searchPaths += dyldLibPath;
-    }
-    dyldLibPath = std::getenv("DYLD_FALLBACK_LIBRARY_PATH");
-    if (dyldLibPath != 0) {
-        if (!searchPaths.empty() && searchPaths[searchPaths.size()-1] != ':')
-            searchPaths += ":";
-        searchPaths += dyldLibPath;
-    }
-    if (!searchPaths.empty()) {
-        std::stringstream ss(searchPaths);
-        std::string item;
-        while (std::getline(ss, item, ':')) {
-            if (item[item.size()-1] != '/')
-                item += "/";
-            paths.push_back(item);
-        }
-    }
-}
-
-// if some libs are missing prefixes, then more stuff will be necessary to do
-bool missing_prefixes = false;
-
 Dependency::Dependency(std::string path, std::string dependent_file) : is_framework(false)
 {
     char original_file_buffer[PATH_MAX];
@@ -93,6 +56,9 @@ Dependency::Dependency(std::string path, std::string dependent_file) : is_framew
     prefix = filePrefix(original_file);
     filename = stripPrefix(original_file);
 
+    if (!prefix.empty() && prefix[prefix.size()-1] != '/')
+        prefix += "/";
+
     // check if this dependency is in /usr/lib, /System/Library, or in ignored list
     if (!Settings::isPrefixBundled(prefix))
         return;
@@ -102,8 +68,8 @@ Dependency::Dependency(std::string path, std::string dependent_file) : is_framew
         std::string framework_root = getFrameworkRoot(original_file);
         std::string framework_path = getFrameworkPath(original_file);
         std::string framework_name = stripPrefix(framework_root);
-        filename = framework_name + "/" + framework_path;
         prefix = filePrefix(framework_root);
+        filename = framework_name + "/" + framework_path;
         if (Settings::verboseOutput()) {
             std::cout << "framework root: " << framework_root << std::endl;
             std::cout << "framework path: " << framework_path << std::endl;
@@ -112,20 +78,20 @@ Dependency::Dependency(std::string path, std::string dependent_file) : is_framew
     }
 
     // check if the lib is in a known location
-    if (!prefix.empty() && prefix[prefix.size()-1] != '/')
-        prefix += "/";
-
     if (prefix.empty() || !fileExists(prefix+filename)) {
         // the paths contains at least /usr/lib so if it is empty we have not initialized it
-        if (paths.empty())
+        size_t search_path_count = Settings::searchPathCount();
+        if (search_path_count == 0)
             initSearchPaths();
 
         // check if file is contained in one of the paths
-        for (size_t i=0; i<paths.size(); ++i) {
-            if (fileExists(paths[i]+filename)) {
-                warning_msg += "FOUND " + filename + " in " + paths[i] + "\n";
-                prefix = paths[i];
-                missing_prefixes = true;
+        search_path_count = Settings::searchPathCount();
+        for (size_t i=0; i<search_path_count; ++i) {
+            std::string search_path = Settings::searchPath(i);
+            if (fileExists(search_path+filename)) {
+                warning_msg += "FOUND " + filename + " in " + search_path + "\n";
+                prefix = search_path;
+                Settings::missingPrefixes(true);
                 break;
             }
         }
@@ -140,8 +106,8 @@ Dependency::Dependency(std::string path, std::string dependent_file) : is_framew
             std::cerr << "\n/!\\ WARNING: Dependency " << filename << " of " << dependent_file << " not found\n";
         if (Settings::verboseOutput())
             std::cout << "     path: " << (prefix+filename) << std::endl;
-        missing_prefixes = true;
-        paths.push_back(getUserInputDirForFile(filename));
+        Settings::missingPrefixes(true);
+        Settings::addSearchPath(getUserInputDirForFile(filename));
     }
 
     new_name = filename;
@@ -188,8 +154,6 @@ void Dependency::copyYourself()
 {
     std::string original_path = getOriginalPath();
     std::string dest_path = getInstallPath();
-    std::string inner_path = getInnerPath();
-    std::string install_path = getInstallPath();
 
     if (is_framework) {
         original_path = getFrameworkRoot(original_path);
@@ -197,33 +161,31 @@ void Dependency::copyYourself()
     }
 
     if (Settings::verboseOutput()) {
+        std::string inner_path = getInnerPath();
         std::cout << "original path: " << original_path << std::endl;
         std::cout << "inner path:    " << inner_path << std::endl;
         std::cout << "dest_path:     " << dest_path << std::endl;
-        std::cout << "install path:  " << install_path << std::endl;
+        std::cout << "install path:  " << getInstallPath() << std::endl;
     }
 
     copyFile(original_path, dest_path);
 
     if (is_framework) {
         std::string headers_path = dest_path + std::string("/Headers");
-        std::string headers_realpath = headers_path;
         char buffer[PATH_MAX];
 
         if (realpath(rtrim(headers_path).c_str(), buffer))
-            headers_realpath = buffer;
+            headers_path = buffer;
 
         if (Settings::verboseOutput())
-            std::cout << "headers path:  " << headers_realpath << std::endl;
+            std::cout << "headers path:  " << headers_path << std::endl;
 
         deleteFile(headers_path, true);
-        deleteFile(headers_realpath, true);
-
         deleteFile(dest_path + "/*.prl");
     }
 
     // fix the lib's inner name
-    changeId(install_path, "@rpath/"+new_name);
+    changeId(getInstallPath(), "@rpath/"+new_name);
 }
 
 void Dependency::fixFileThatDependsOnMe(std::string file_to_fix)
@@ -236,7 +198,7 @@ void Dependency::fixFileThatDependsOnMe(std::string file_to_fix)
     }
 
     // TODO: revise
-    if (missing_prefixes) {
+    if (Settings::missingPrefixes()) {
         // for main lib file
         changeInstallName(file_to_fix, filename, getInnerPath());
         // for symlinks
diff --git a/src/DylibBundler.cpp b/src/DylibBundler.cpp
index f7dd0f9..d7f60f0 100644
--- a/src/DylibBundler.cpp
+++ b/src/DylibBundler.cpp
@@ -234,7 +234,7 @@ void addDependency(std::string path, std::string dependent_file)
 }
 
 // Fill |lines| with dependencies of given |filename|
-void collectDependencies(std::string dependent_file, std::vector<std::string>& lines)
+void collectDependencies(const std::string& dependent_file, std::vector<std::string>& lines)
 {
     std::string cmd = "otool -l " + dependent_file;
     std::string output = systemOutput(cmd);
@@ -268,19 +268,17 @@ void collectDependencies(std::string dependent_file, std::vector<std::string>& l
     }
 }
 
-void collectDependencies(std::string dependent_file)
+void collectDependencies(const std::string& dependent_file)
 {
     std::vector<std::string> lines;
     collectDependencies(dependent_file, lines);
 
     for (size_t i=0; i<lines.size(); ++i) {
-        if (!Settings::bundleFrameworks()) {
-            if (lines[i].find(".framework") != std::string::npos)
-                continue;
-        }
         // lines containing path begin with a tab
         if (lines[i][0] != '\t')
             continue;
+        if (!Settings::isPrefixBundled(lines[i]))
+            continue;
         // trim useless info, keep only library path
         std::string dep_path = lines[i].substr(1, lines[i].rfind(" (") - 1);
         if (isRpath(dep_path))
@@ -313,18 +311,16 @@ void collectSubDependencies()
                 original_path = searchFilenameInRpaths(original_path);
 
             collectRpathsForFilename(original_path);
-
             std::vector<std::string> lines;
             collectDependencies(original_path, lines);
 
             for (size_t i=0; i<lines.size(); ++i) {
-                if (!Settings::bundleFrameworks()) {
-                    if (lines[i].find(".framework") != std::string::npos)
-                        continue;
-                }
                 // lines containing path begin with a tab
                 if (lines[i][0] != '\t')
                     continue;
+                // skip system/ignored prefixes
+                if (!Settings::isPrefixBundled(lines[i]))
+                    continue;
                 // trim useless info, keep only library name
                 std::string dep_path = lines[i].substr(1, lines[i].rfind(" (") - 1);
                 if (isRpath(dep_path)) {
diff --git a/src/DylibBundler.h b/src/DylibBundler.h
index 3c0922e..3c43d12 100644
--- a/src/DylibBundler.h
+++ b/src/DylibBundler.h
@@ -14,7 +14,8 @@ std::string searchFilenameInRpaths(const std::string& rpath_file);
 void fixRpathsOnFile(const std::string& original_file, const std::string& file_to_fix);
 
 void addDependency(std::string path, std::string dependent_file);
-void collectDependencies(std::string dependent_file);
+void collectDependencies(const std::string& dependent_file, std::vector<std::string>& lines);
+void collectDependencies(const std::string& dependent_file);
 void collectSubDependencies();
 
 void doneWithDeps_go();
diff --git a/src/Settings.cpp b/src/Settings.cpp
index 5837327..2769a39 100644
--- a/src/Settings.cpp
+++ b/src/Settings.cpp
@@ -11,18 +11,22 @@ bool verbose_output = false;
 bool bundle_libs = true;
 bool bundle_frameworks = false;
 
-std::string dest_folder_str = "Frameworks";
-std::string inside_path_str = "@executable_path/../Frameworks/";
+std::string dest_folder_str = "./libs/";
+std::string dest_folder_str_app = "./Frameworks/";
+std::string dest_folder = dest_folder_str;
+std::string dest_path = dest_folder;
+
+std::string inside_path_str = "@executable_path/../libs/";
+std::string inside_path_str_app = "@executable_path/../Frameworks/";
+std::string inside_path = inside_path_str;
 
 std::string app_bundle;
-std::string dest_folder;
-
+bool appBundleProvided() { return !app_bundle.empty(); }
 std::string appBundle() { return app_bundle; }
 void appBundle(std::string path) {
     app_bundle = path;
-    // fix path if needed so it ends with '/'
     if (app_bundle[app_bundle.size()-1] != '/')
-        app_bundle += "/";
+        app_bundle += "/"; // fix path if needed so it ends with '/'
 
     std::string cmd = "/usr/libexec/PlistBuddy -c 'Print :CFBundleExecutable' ";
     cmd += app_bundle + "Contents/Info.plist";
@@ -30,60 +34,63 @@ void appBundle(std::string path) {
 
     addFileToFix(app_bundle + "Contents/MacOS/" + bundle_executable);
 
-    // fix path if needed so it ends with '/'
-    if (dest_folder_str[dest_folder_str.size()-1] != '/')
-        dest_folder_str += "/";
-    dest_folder = app_bundle + "Contents/" + dest_folder_str;
+    if (inside_path == inside_path_str)
+        inside_path = inside_path_str_app;
+    if (dest_folder == dest_folder_str)
+        dest_folder = dest_folder_str_app;
+
+    dest_path = app_bundle + "Contents/" + dest_folder;
+    char buffer[PATH_MAX];
+    if (realpath(dest_path.c_str(), buffer))
+        dest_path = buffer;
+    if (dest_path[dest_path.size()-1] != '/')
+        dest_path += "/";
 }
 
-std::string destFolder() { return dest_folder; }
+std::string destFolder() { return dest_path; }
 void destFolder(std::string path)
 {
-    dest_folder_str = path;
-    // fix path if needed so it ends with '/'
-    if (dest_folder_str[dest_folder_str.size()-1] != '/')
-        dest_folder_str += "/";
-    dest_folder = dest_folder_str;
-    if (!app_bundle.empty())
-        dest_folder = app_bundle + "Contents/" + dest_folder_str;
+    if (path[path.size()-1] != '/')
+        path += "/";
+    dest_folder = path;
+    if (appBundleProvided()) {
+        char buffer[PATH_MAX];
+        std::string dest_path = app_bundle + "Contents/" + path;
+        if (realpath(dest_path.c_str(), buffer))
+            dest_path = buffer;
+        if (dest_path[dest_path.size()-1] != '/')
+            dest_path += "/";
+        dest_folder = dest_path;
+    }
 }
 
 std::string executableFolder() { return app_bundle + "Contents/MacOS/"; }
-
 std::string frameworksFolder() { return app_bundle + "Contents/Frameworks/"; }
-
 std::string pluginsFolder() { return app_bundle + "Contents/PlugIns/"; }
-
 std::string resourcesFolder() { return app_bundle + "Contents/Resources/"; }
 
 std::vector<std::string> files;
-
 void addFileToFix(std::string path) { files.push_back(path); }
-
 std::string fileToFix(const int n) { return files[n]; }
-
 std::vector<std::string> filesToFix() { return files; }
-
 size_t filesToFixCount() { return files.size(); }
 
-std::string insideLibPath() { return inside_path_str; }
+std::string insideLibPath() { return inside_path; }
 void insideLibPath(std::string p)
 {
-    inside_path_str = p;
+    inside_path = p;
     // fix path if needed so it ends with '/'
-    if (inside_path_str[inside_path_str.size()-1] != '/')
-        inside_path_str += "/";
+    if (inside_path[inside_path.size()-1] != '/')
+        inside_path += "/";
 }
 
 std::vector<std::string> prefixes_to_ignore;
-
 void ignorePrefix(std::string prefix)
 {
     if (prefix[prefix.size()-1] != '/')
         prefix += "/";
     prefixes_to_ignore.push_back(prefix);
 }
-
 bool isPrefixIgnored(std::string prefix)
 {
     for (size_t n=0; n<prefixes_to_ignore.size(); n++) {
@@ -134,4 +141,9 @@ void quietOutput(bool status) { quiet_output = status; }
 bool verboseOutput() { return verbose_output; }
 void verboseOutput(bool status) { verbose_output = status; }
 
+// if some libs are missing prefixes, then more stuff will be necessary to do
+bool missing_prefixes = false;
+bool missingPrefixes() { return missing_prefixes; }
+void missingPrefixes(bool status) { missing_prefixes = status; }
+
 } // namespace Settings
diff --git a/src/Settings.h b/src/Settings.h
index efad96e..931edb6 100644
--- a/src/Settings.h
+++ b/src/Settings.h
@@ -54,6 +54,9 @@ void quietOutput(bool status);
 bool verboseOutput();
 void verboseOutput(bool status);
 
+bool missingPrefixes();
+void missingPrefixes(bool status);
+
 } // namespace Settings
 
 #endif
diff --git a/src/Utils.cpp b/src/Utils.cpp
index 9d6429a..209509e 100644
--- a/src/Utils.cpp
+++ b/src/Utils.cpp
@@ -3,6 +3,7 @@
 #include <cstdio>
 #include <cstdlib>
 #include <iostream>
+#include <sstream>
 
 #include <stdio.h>
 #include <sys/stat.h>
@@ -290,3 +291,33 @@ std::string getUserInputDirForFile(const std::string& filename)
         }
     }
 }
+
+void initSearchPaths()
+{
+    // check the same paths the system would search for dylibs
+    std::string searchPaths;
+    char *dyldLibPath = std::getenv("DYLD_LIBRARY_PATH");
+    if (dyldLibPath != 0)
+        searchPaths = dyldLibPath;
+    dyldLibPath = std::getenv("DYLD_FALLBACK_FRAMEWORK_PATH");
+    if (dyldLibPath != 0) {
+        if (!searchPaths.empty() && searchPaths[searchPaths.size()-1] != ':')
+            searchPaths += ":";
+        searchPaths += dyldLibPath;
+    }
+    dyldLibPath = std::getenv("DYLD_FALLBACK_LIBRARY_PATH");
+    if (dyldLibPath != 0) {
+        if (!searchPaths.empty() && searchPaths[searchPaths.size()-1] != ':')
+            searchPaths += ":";
+        searchPaths += dyldLibPath;
+    }
+    if (!searchPaths.empty()) {
+        std::stringstream ss(searchPaths);
+        std::string item;
+        while (std::getline(ss, item, ':')) {
+            if (item[item.size()-1] != '/')
+                item += "/";
+            Settings::addSearchPath(item);
+        }
+    }
+}
diff --git a/src/Utils.h b/src/Utils.h
index 7557e92..ba37a2f 100644
--- a/src/Utils.h
+++ b/src/Utils.h
@@ -39,4 +39,7 @@ bool mkdir(std::string path);
 void createDestDir();
 std::string getUserInputDirForFile(const std::string& filename);
 
+// check the same paths the system would search for dylibs
+void initSearchPaths();
+
 #endif