Squashed commit of the following:

commit 3dbe798285f95dc63ae33739df5daadb8c432f24
Author: Valerio Virgillito <valerio@motorola.com>
Date:   Tue Feb 28 16:20:25 2012 -0800

    putting the color panel on top when opening ninja

    Signed-off-by: Valerio Virgillito <valerio@motorola.com>

commit b5ae7f0babb185051242df47634e24ad7a68f60e
Merge: 20d4f1d 2bc8343
Author: Valerio Virgillito <valerio@motorola.com>
Date:   Tue Feb 28 16:15:44 2012 -0800

    Merge branch 'nested-selection' of https://github.com/mencio/ninja-internal into integration-candidate

    Conflicts:
    	js/ninja.reel/ninja.html

    Signed-off-by: Valerio Virgillito <valerio@motorola.com>

commit 2bc834334a3197ab7cffacc7332eafd1b52443d1
Author: Valerio Virgillito <valerio@motorola.com>
Date:   Tue Feb 28 16:11:42 2012 -0800

    revert changes to the timeline

    Signed-off-by: Valerio Virgillito <valerio@motorola.com>

commit ae96ea66acc4be873fb7fb73fb3f4484b6db3eb8
Author: Valerio Virgillito <valerio@motorola.com>
Date:   Tue Feb 28 16:03:32 2012 -0800

    adding some margin to the bread crumb buttons

    Signed-off-by: Valerio Virgillito <valerio@motorola.com>

commit 20d4f1d703c004dd7f869576b6c471b3fb5b5d3e
Merge: ee52f19 557c4d3
Author: Valerio Virgillito <valerio@motorola.com>
Date:   Tue Feb 28 16:02:37 2012 -0800

    Merge pull request #81 from ananyasen/integration-candidate

    persist selections while switching documents

commit 557c4d3100ccde51b925b71f0650b2c783a4a042
Author: Ananya Sen <Ananya.Sen@motorola.com>
Date:   Tue Feb 28 16:02:15 2012 -0800

    minor fix for handling selections on switch document

    Signed-off-by: Ananya Sen <Ananya.Sen@motorola.com>

commit a230f0cd065613a1bc933e3d6d3f7e77f52bec04
Author: Ananya Sen <Ananya.Sen@motorola.com>
Date:   Tue Feb 28 15:48:55 2012 -0800

    selection controller sets _isDocument = true if number of selections are 0, on switch document

    Signed-off-by: Ananya Sen <Ananya.Sen@motorola.com>

commit ee52f197d1eb53a5ff30b54b8df1d2b53014eb0e
Merge: 8e370cc da83f44
Author: Valerio Virgillito <valerio@motorola.com>
Date:   Tue Feb 28 15:16:12 2012 -0800

    Merge pull request #80 from joseeight/FileIO-Build-Candidate

    Adding CSS <link> attributes support to I/O

commit 5ab7efb9949e486395659c383064a08821febdae
Author: Ananya Sen <Ananya.Sen@motorola.com>
Date:   Tue Feb 28 15:15:27 2012 -0800

    persist selections while switching documents

    Signed-off-by: Ananya Sen <Ananya.Sen@motorola.com>

commit da83f44b0ecf379b0950a88d1c378fbedb80e386
Merge: b799b7c 676b4e2
Author: Jose Antonio Marquez <kgq387@motorola.com>
Date:   Tue Feb 28 15:15:12 2012 -0800

    Merge branch 'refs/heads/integration-candidate' into FileIO-Build-Candidate

commit 8e370cc72aa85de594a5d55ae89947a70af414ca
Merge: 8de4002 676b4e2
Author: Valerio Virgillito <valerio@motorola.com>
Date:   Tue Feb 28 15:08:48 2012 -0800

    Merge branch 'integration-candidate' of github.com:Motorola-Mobility/ninja-internal into integration-candidate

commit 8de40029442333114d81ac30a8886a995a3dc56b
Merge: b0b4d64 eb27ed3
Author: Valerio Virgillito <valerio@motorola.com>
Date:   Tue Feb 28 15:08:18 2012 -0800

    Merge branch 'ToolFixes' of https://github.com/mqg734/ninja-internal into integration-candidate

commit eb27ed35bf282262843de13b00af89a2bceac53f
Merge: ea59626 7c9291a
Author: Nivesh Rajbhandari <mqg734@motorola.com>
Date:   Tue Feb 28 15:04:33 2012 -0800

    Merge branch 'refs/heads/ninja-internal' into ToolFixes

commit b799b7cf3a422f407045c52a4c6a61756d1ea096
Merge: f7c08fe 2ce9f65
Author: Jose Antonio Marquez <kgq387@motorola.com>
Date:   Tue Feb 28 15:03:38 2012 -0800

    Merge branch 'refs/heads/FileIO' into FileIO-Build-Candidate

commit 2ce9f65c3a34937928f08690606962af3085c74f
Author: Jose Antonio Marquez <kgq387@motorola.com>
Date:   Tue Feb 28 15:03:23 2012 -0800

    CSS attributes

    Setting up logic to include attributes in <link> for the <style> duplicates and add attributes created in Ninja back to <link> tag on save.

commit ea5962641519b9d32499c4440112e7fa821e3a79
Author: Nivesh Rajbhandari <mqg734@motorola.com>
Date:   Tue Feb 28 15:02:57 2012 -0800

    Fix for "jumping" issue when using the selection tool repeatedly.

    Signed-off-by: Nivesh Rajbhandari <mqg734@motorola.com>

commit 676b4e2d7091ac63ce06f51be686b902b940bfff
Merge: b0b4d64 f2ab699
Author: Valerio Virgillito <valerio@motorola.com>
Date:   Tue Feb 28 14:55:17 2012 -0800

    Merge pull request #79 from pushkarjoshi/pentool

    Pentool

commit f2ab6999a9fdaa18056fb5a148ef1bcaefb7d854
Author: Pushkar Joshi <pushkar@motorola.com>
Date:   Tue Feb 28 14:53:33 2012 -0800

    reverting manifest name

commit 63307c9abf120985d979a40a53a0598d3f0d5c5a
Merge: e1a65d0 7c9291a
Author: Pushkar Joshi <pushkar@motorola.com>
Date:   Tue Feb 28 14:01:05 2012 -0800

    Merge branch 'master' into pentool

    Conflicts:
    	manifest.json

commit e1a65d0c2a13e12ee53be98c731616e35aa07a41
Author: Pushkar Joshi <pushkar@motorola.com>
Date:   Tue Feb 28 13:58:34 2012 -0800

    new anchor control guide rendering (smaller handles)

    and
    clamp min. width and height to 1 while resizing subpaths

commit b0b4d6492d6ddd3b7ab39c2f4d1c01b8e9bacfb6
Merge: 7cafa04 538db48
Author: Valerio Virgillito <valerio@motorola.com>
Date:   Tue Feb 28 13:41:12 2012 -0800

    Merge pull request #78 from imix23ways/Timeline

    Timeline bug fixes

commit 933ed4c880128eed80bdc6372eb1dfdb23af4c37
Merge: 6af71de 7c9291a
Author: Jose Antonio Marquez <kgq387@motorola.com>
Date:   Tue Feb 28 13:33:45 2012 -0800

    Merge branch 'refs/heads/NinjaInternal' into FileIO

commit f7c08fe5a8424d8c7837a4e3a975e63bcddc3b14
Merge: 811d509 7c9291a
Author: Jose Antonio Marquez <kgq387@motorola.com>
Date:   Tue Feb 28 13:33:17 2012 -0800

    Merge branch 'refs/heads/NinjaInternal' into FileIO-Build-Candidate

commit 7cafa0464ee0c1621ffea04c2192f19008c9fc49
Merge: 2ab07cb 811d509
Author: Valerio Virgillito <valerio@motorola.com>
Date:   Tue Feb 28 13:20:44 2012 -0800

    Merge branch 'FileIO-Build-Candidate' of https://github.com/joseeight/ninja-internal into integration-candidate

commit 2ab07cb8ac76a06606ce455bb2e6b4889e3ddc65
Merge: e5b1102 347fc28
Author: Valerio Virgillito <valerio@motorola.com>
Date:   Tue Feb 28 13:19:52 2012 -0800

    Merge branch 'integration' of https://github.com/ericmueller/ninja-internal into integration-candidate

commit e5b1102f0cff7f5ba7074840ccf29dc1c02ced8e
Merge: 7c9291a a70c628
Author: Valerio Virgillito <valerio@motorola.com>
Date:   Tue Feb 28 13:17:55 2012 -0800

    Merge branch 'ToolFixes' of https://github.com/mqg734/ninja-internal into integration-candidate

commit 347fc28227d822e9fea3fa823fae79cf14ea041c
Merge: ed16298 7c9291a
Author: hwc487 <hwc487@motorola.com>
Date:   Tue Feb 28 12:58:09 2012 -0800

    Merge branch 'master' of github.com:Motorola-Mobility/ninja-internal into integration

commit 7cbd26d475eaad817042692f9116f9a24ae60997
Author: Pushkar Joshi <pushkar@motorola.com>
Date:   Tue Feb 28 10:24:06 2012 -0800

    Bug fixes:

    1152: allow deleting of multiple paths from inside pen tool
    1128: keyboard hotkey shortcut 'P' for pen tool
    941: changing width or height of the path scales the path

commit ed16298e4323b733f6dc957c307dc07036fa3569
Merge: b194efa 6054d13
Author: hwc487 <hwc487@motorola.com>
Date:   Tue Feb 28 09:55:07 2012 -0800

    Merge branch 'master' of github.com:Motorola-Mobility/ninja-internal into integration

commit 19e94dc51a279501352a08d511b18144f83500e5
Author: Valerio Virgillito <valerio@motorola.com>
Date:   Tue Feb 28 00:47:46 2012 -0800

    cleanup and fixing selecting each bread crumb

    Signed-off-by: Valerio Virgillito <valerio@motorola.com>

commit 6af71de5b80fd531901e82b12372446b569902d8
Merge: f872077 6054d13
Author: Jose Antonio Marquez <kgq387@motorola.com>
Date:   Mon Feb 27 21:44:45 2012 -0800

    Merge branch 'refs/heads/NinjaInternal' into FileIO

commit db5db0a92c1fb67eac262c33d4fbf776ceabbb3c
Author: Valerio Virgillito <valerio@motorola.com>
Date:   Mon Feb 27 21:17:29 2012 -0800

    breadcrumb cleanup and moving the resized on top of the timeline panel

    Signed-off-by: Valerio Virgillito <valerio@motorola.com>

commit a70c62891d0c7dd032d9382c50d1555ab81c4e33
Author: Nivesh Rajbhandari <mqg734@motorola.com>
Date:   Mon Feb 27 16:24:13 2012 -0800

    Fixing tooltips and keyboard shortcuts for 3d tools.

    IKNinja-1014 and IKNinja-1015.

    Signed-off-by: Nivesh Rajbhandari <mqg734@motorola.com>

commit ef38731ae2769dcb2247db599cdfe62d38e34b28
Author: Nivesh Rajbhandari <mqg734@motorola.com>
Date:   Mon Feb 27 15:39:16 2012 -0800

    Reset translation values as well when double-clicking to reset the rotation values.

    Signed-off-by: Nivesh Rajbhandari <mqg734@motorola.com>

commit 811d5092345bf520f6a683eec89cf7d8ed7aa490
Merge: ceba159 f872077
Author: Jose Antonio Marquez <kgq387@motorola.com>
Date:   Mon Feb 27 14:39:10 2012 -0800

    Merge branch 'refs/heads/FileIO' into FileIO-Build-Candidate

commit f872077e947916496235f4e871511ce890953d04
Author: Jose Antonio Marquez <kgq387@motorola.com>
Date:   Mon Feb 27 14:38:59 2012 -0800

    Updating legal copy

commit ceba159acedcaada47f990392b3bbebc2025e40a
Merge: a564d96 3e2889b
Author: Jose Antonio Marquez <kgq387@motorola.com>
Date:   Mon Feb 27 14:29:53 2012 -0800

    Merge branch 'refs/heads/FileIO' into FileIO-Build-Candidate

commit 3e2889b94d5e6af93ec0eaca114802e30c8c38ef
Author: Jose Antonio Marquez <kgq387@motorola.com>
Date:   Mon Feb 27 14:29:17 2012 -0800

    Updating credits

commit affdf784f3dae1febe279a214857e6fe3ba56db1
Merge: 7e63b5d 15d00c4
Author: Jose Antonio Marquez Russo <jose@eightyearproject.com>
Date:   Mon Feb 27 14:28:59 2012 -0800

    Merge pull request #21 from ananyasen/FileIO

    FileIO branch pull request

commit 15d00c49b522aa471d1ccfbbd33f5c0e721eb89e
Merge: 604ace9 7e63b5d
Author: Ananya Sen <Ananya.Sen@motorola.com>
Date:   Mon Feb 27 14:24:49 2012 -0800

    Merge branch 'refs/heads/FileIO-jose' into FileIO

commit a564d969ffcb7bc0dd701a1ef653f666ae857f77
Merge: c65eb4b 7e63b5d
Author: Jose Antonio Marquez <kgq387@motorola.com>
Date:   Mon Feb 27 14:11:09 2012 -0800

    Merge branch 'refs/heads/FileIO' into FileIO-Build-Candidate

commit 7e63b5d0b6990b6c0ec0385d35534b91982ac672
Author: Jose Antonio Marquez <kgq387@motorola.com>
Date:   Mon Feb 27 14:10:53 2012 -0800

    Cleaning up pretty functions in IO

commit b194efa0556806593b29eb197250df462e89fcc4
Author: hwc487 <hwc487@motorola.com>
Date:   Mon Feb 27 14:03:11 2012 -0800

    Enable shift key constraint for Pan Tool.

commit 124ad4709780013615d2ff1da05ace9887ee7709
Merge: a8bd158 8125c8c
Author: hwc487 <hwc487@motorola.com>
Date:   Mon Feb 27 13:41:31 2012 -0800

    Merge branch 'master' of github.com:Motorola-Mobility/ninja-internal into integration

commit a8bd1585ae83d4d304b9f9f41823bb3dcbff9e01
Author: hwc487 <hwc487@motorola.com>
Date:   Mon Feb 27 12:14:29 2012 -0800

    Color fix for line shapes.

commit 604ace9cfc9fae6b6c121259523a9060c5306161
Author: Ananya Sen <Ananya.Sen@motorola.com>
Date:   Mon Feb 27 11:59:58 2012 -0800

    - save show3DGrid flag per document while switching documents
    - fix zoom tool keyboard control to listen to Z when ctrl and shift keys are not pressed with it

    Signed-off-by: Ananya Sen <Ananya.Sen@motorola.com>

commit bfa895634324a78652f2a7eecf725d9c6030023f
Author: hwc487 <hwc487@motorola.com>
Date:   Mon Feb 27 11:58:44 2012 -0800

    Changed the hardcoded publish setting for a PI fix.

commit 8578322c60adaaf65f37ba96f2a0f7ed9de8e1dc
Author: hwc487 <hwc487@motorola.com>
Date:   Mon Feb 27 10:28:03 2012 -0800

    Fixed various rendering bugs.

commit 544dec04fd379b10eff254bbdd105bfaf828f8a5
Author: Jose Antonio Marquez <kgq387@motorola.com>
Date:   Sun Feb 26 12:12:22 2012 -0800

    Cleaning up and adding TODOs

commit 053fc63a2950c7a5ee4ebf98033b64d474a3c46e
Merge: a5ba66e 23a2219
Author: Pushkar Joshi <pushkar@motorola.com>
Date:   Fri Feb 24 12:03:51 2012 -0800

    Merge branch 'master' into pentool

commit a5ba66ecefa9c9c17e0f5e1725e2141f7a3540a2
Author: Pushkar Joshi <pushkar@motorola.com>
Date:   Fri Feb 24 12:01:03 2012 -0800

    adding unpacked to the manifest file (to differentiate from the ninjateam (main) chrome app)

commit d0661d6c587aced68a68e36a5ec4e81f8a2096e8
Author: hwc487 <hwc487@motorola.com>
Date:   Thu Feb 23 16:57:55 2012 -0800

    bug fixes for canvas 2d shape drawing.

Signed-off-by: Jonathan Duran <jduran@motorola.com>

2 files changed, 73 insertions, 31 deletions

diff --git a/js/mediators/io-mediator.js b/js/mediators/io-mediator.js
index 30180155..6b26668b 100644
--- a/js/mediators/io-mediator.js
+++ b/js/mediators/io-mediator.js
@@ -146,22 +146,27 @@ exports.IoMediator = Montage.create(Component, {
                                 //Copy webGL library if needed
                                 if (file.webgl.length > 0) {
                                         for (var i in this.application.ninja.coreIoApi.ninjaLibrary.libs) {
-                                                //if (this.application.ninja.coreIoApi.ninjaLibrary.libs[i].name === 'Assets' || this.application.ninja.coreIoApi.ninjaLibrary.libs[i].name === 'RDGE') {
+                                                //Checking for RDGE library to be available
                                                 if (this.application.ninja.coreIoApi.ninjaLibrary.libs[i].name === 'RDGE') {
                                                         this.application.ninja.coreIoApi.ninjaLibrary.copyLibToCloud(file.document.root, (this.application.ninja.coreIoApi.ninjaLibrary.libs[i].name+this.application.ninja.coreIoApi.ninjaLibrary.libs[i].version).toLowerCase());
+                                                } else {
+                                                        //TODO: Error handle no available library to copy
                                                 }
                                         }
                                 }
-                                //
+                                
+                                //TODO: Add check for Monatage library to copy
+                                
+                                //Getting content from function to properly handle saving assets (as in external if flagged)
                                 contents = this.parseNinjaTemplateToHtml(file);
                                 break;
                         default:
                                 contents = file.content;
                                 break;
                 }
-                //
+                //Making call to save file
                 save = this.fio.saveFile({uri: file.document.uri, contents: contents});
-            //
+            //Checking for callback
             if (callback) callback(save);
         }
     },
@@ -170,7 +175,7 @@ exports.IoMediator = Montage.create(Component, {
     fileSaveAs: {
         enumerable: false,
         value: function (copyTo, copyFrom, callback) {
-                //
+                //TODO: Implement Save As functionality
         }
     },
     ////////////////////////////////////////////////////////////////////
@@ -178,7 +183,7 @@ exports.IoMediator = Montage.create(Component, {
     fileDelete: {
         enumerable: false,
         value: function (file, callback) {
-                //
+                //TODO: Implement Delete functionality
         }
     },
     ////////////////////////////////////////////////////////////////////
@@ -205,7 +210,7 @@ exports.IoMediator = Montage.create(Component, {
                 //Getting all CSS (style or link) tags
                 var styletags = template.document.content.document.getElementsByTagName('style'),
                         linktags = template.document.content.document.getElementsByTagName('link'),
-                        url = new RegExp(chrome.extension.getURL('js/document/templates/montage-html/'), 'gi');
+                        url = new RegExp(chrome.extension.getURL('js/document/templates/montage-html/'), 'gi'); //TODO: Make public into var
                 //Looping through link tags and removing file recreated elements
                 for (var j in styletags) {
                         if (styletags[j].getAttribute) {
@@ -255,6 +260,17 @@ exports.IoMediator = Montage.create(Component, {
                         var styleCounter = 0,
                                 docStyles = template.document.content.document.getElementsByTagName('style'),
                                 docLinks = template.document.content.document.getElementsByTagName('link');
+                        //Removing Ninja Data Attributes
+                        for (var n in docLinks) {
+                                if (docLinks[n].attributes) {
+                                        for (var m in docLinks[n].attributes) {
+                                                        if (docLinks[n].attributes[m].name && docLinks[n].attributes[m].name.indexOf('data-ninja')!=-1) {
+                                                                docLinks[n].removeAttribute(docLinks[n].attributes[m].name);
+                                                        }
+                                                }
+                                }
+                        }
+                        //
                         for(var i in template.css) {
                                 if (template.css[i].ownerNode) {
                                         if (template.css[i].ownerNode.getAttribute) {
@@ -263,6 +279,22 @@ exports.IoMediator = Montage.create(Component, {
                                                         docStyles[styleCounter].innerHTML = this.getCssFromRules(template.css[i].cssRules);
                                                         styleCounter++;
                                                 } else {
+                                                        //Checking for attributes to be added to tag upon saving
+                                                        for (var k in docLinks) {
+                                                                if (docLinks[k].getAttribute) {
+                                                                        if (docLinks[k].getAttribute('href') && ('/'+docLinks[k].getAttribute('href')) === template.css[i].ownerNode.getAttribute('data-ninja-file-url')) {
+                                                                                for (var l in template.css[i].ownerNode.attributes) {
+                                                                                        if (template.css[i].ownerNode.attributes[l].value) {
+                                                                                                if (template.css[i].ownerNode.attributes[l].name.indexOf('data-ninja')!=-1) {
+                                                                                                        //Ninja attribute...
+                                                                                                } else {
+                                                                                                        docLinks[k].setAttribute(template.css[i].ownerNode.attributes[l].name, template.css[i].ownerNode.attributes[l].value);
+                                                                                                }
+                                                                                        }
+                                                                                }
+                                                                        }
+                                                                }
+                                                        }
                                                         //Saving data from rules array converted to string into <link> file
                                                         var save = this.fio.saveFile({uri: template.css[i].ownerNode.getAttribute('data-ninja-uri'), contents: this.getCssFromRules(template.css[i].cssRules)});
                                                 }
@@ -313,7 +345,7 @@ exports.IoMediator = Montage.create(Component, {
                         webgltag.innerHTML = json;
                 }
                 //
-                return this.getPretyHtml(template.document.content.document.documentElement.outerHTML.replace(url, ''));
+                return this.getPrettyHtml(template.document.content.document.documentElement.outerHTML.replace(url, ''));
         }
     },
     ////////////////////////////////////////////////////////////////////
@@ -333,14 +365,19 @@ exports.IoMediator = Montage.create(Component, {
                 //TODO: Add better logic for creating this string
                 url = new RegExp(chrome.extension.getURL('js/document/templates/montage-html/'), 'gi');
                 //Returning the CSS string
-                return this.getPretyCss(css.replace(url, ''));
+                return this.getPrettyCss(css.replace(url, ''));
         }
     },
     ////////////////////////////////////////////////////////////////////
-    //Using prettification code from http://jsbeautifier.org
+    ////////////////////////////////////////////////////////////////////
+    //Pretty methods (minified)
     /*
-        Copyright (c) 2009 - 2011, Einar Lielmanis
-
+                is-beautify javascript code courtesy of Einar Lielmanis:
+                Code from https://github.com/einars/js-beautify
+                License https://github.com/einars/js-beautify/blob/master/license.txt
+                Used with author's permission, as stated below
+                
+                Copyright (c) 2009 - 2011, Einar Lielmanis
                 Permission is hereby granted, free of charge, to any person
                 obtaining a copy of this software and associated documentation
                 files (the "Software"), to deal in the Software without