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JavaScript, Reading and Writing files for a locally hosted application

I have read several posts on this site that ask similar questions but the key difference is they involve a client and a server. For my use, this is not the case. I am simply pasting a file directory on my computer into my browser in order to view a local HTML file, packed with CSS and some jQuery.
I've been looking around and the answers I've found are "No; a client can not write to a server", and "No; a server can not write to a client". But there is no answer to "can a client write to a client with JavaScript?"
Use case:
I'm building a webapp (website? JS app?) as a college project for a stock management tool that will be locally hosted and never connect to the internet. Sure, I could knock one together in python in a couple hours, but I wouldn't learn anything. I need to create an access a txt file containing an array of the current stock of all the items so that when the application is loaded, the user doesn't have to manually enter anything but the changes to stock levels.
Honestly, I'm a beginner at JS and JQ and I'm only going off of what makes sense based on a mix of HTML and Python that I know.
Maybe PHP would be the better option for this particular option, or maybe JS will work well enough.

You still won't be doing client-to-client, your browser will just act as though the local file system is the server using the file:// protocol which means the same rules about a "client" (the browser) cannot write to a "server" (your local file system) apply.
If you wan't to be able to write an application that can interface directly with the filesystem, then look into something like Electron which is essentially an augmented website that gives you APIs to interact with the actual computer the app is being run on, including filesystem stuff.

Can NodeJS be used on the web instead of the command-line

When developing a website and doing some server-side stuff with NodeJS can NodeJS be used on the command-line only or can it be used for scripting too? For example creating a script and doing all my NodeJS stuff in there and then including the script in my HTML without the command-line or is this not possible?

You can't embed Node.js in a webpage, but browsers have built in JavaScript runtimes so you don't need to embed another one.
You can't use Node.js specific APIs from JavaScript in a webpage. Most of them have serious security implications (such as providing a means for JavaScript to access the filesystem).
You can use Node.js to run an HTTP server, which you can then access from the browser (both directly and via XMLHttpRequest).

try node-browserify # https://github.com/substack/node-browserify, which i guess a bit closer to what you wanted here.

Possible Autoit-like JavaScript macros?

The title says it all. Is there a way to write macros in JavaScript to achieve a similar functionality to that of Autoit? I just would want to manipulate files on my own computer (offline) and could easily do it with autoit, but since I am currently learning JavaScript -- plan to develop in Node.js -- I figure it wouldn't hurt to get the extra practice.
Thanks guys!

Use an application which supports JavaScript as a shell scripting language, such as the following:
JsRoboKey
PowershellJS
PowerChakra
RemoteNodeJS
JScript + WSH
JavaScript Shell Scripting with JSC
QtScript: QScriptEngine
Part I: How to Choose a JavaScript Engine for iOS and Android Development - OpenAphid-Engine

nodejs has a module which do autoit things --
nodejs install autoit
var au = require('autoit');
au.Init();
au.Run("notepad.exe");
au.WinWait("[Class:Notepad]");
au.Send("Hello, autoit & nodejs!");

NodeJS is a very powerfull platform, it is extensible and opensource.
There is no problem to run local scripts to do everything you need using JavaScript (see standard FileSystem library docs). You can also try to look in NPM(NodeJS package manager).

Assuming you have AutoIt installed (say in folder C:\AU3) and this folder in the PATH, you can add
extension '.AU3' to the PATHEXT environment variable, and create an AutoIt script called, say,
hello.au3 with just a silly line:
MsgBox(0, "Warning", "Hello, World!")
Now, simply typing the command 'hello' will execute the script, displaying the silly message in a modal message box.
Next, create an equally silly Node.js script, say, MyWarn.js - in the same folder:
var oCP = require("child_process");
console.log("Starting...");
var oNP = oCP.execSync("hello");
console.log("Done.");
Assuming Node is also in the PATH, try this command:
node MyWarn
So ... we get the benefits of Node (for its jit), and the benefits of AutoIt (for its GUI handling.)
The problem is getting the two to communicate. Personally, I use a RamDisk to pass small files...

Javascript can't write to a file on your local machine remotely.. Its almost the same as HTML in a view model.
It can however perform some executions of other scripts via AJAX for example. But thats on server again.
It might be worth a look to read on server && client side differences.
im not 100% sure but node might offer another outlet on this but it would still be server side.. Not locally.
The Server - This party is responsible for serving pages and handling the logic | Code behind.
The Client - This party requests pages from the Server, and displays them to the user. On most cases, the client is a web browser.
The User - The user uses the Client in order to surf the web, fill in forms, watch videos online, etc.

Is it possible to convert a mp3 file to m4r with Javascript or jQuery?

Is it possible with Javascript or jQuery to convert mp3, wav, etc. to m4r format?

Let's assume you had a library that can change the format of files.
Let's also assume you only need the application to work on current browsers that implement FileAPI or FileReference so you can have access to uploaded files (you can't have access to them without FileAPI or FileReference unless you use Flash or Java Applets or equivalent technologies).
You wouldn't be able to write the output file back to the user because JavaScript is not allowed to access the local filesystem.
Your only solution would become sending the converted file to the server and the server sending it back to you with a force download directive so that the user will be prompted to download the results.
Now back to if there were a library that can the conversion (or even native JavaScript)... I haven't heard of any. It's not impossible to build one but it is impractical and wouldn't run very fast.
Edit:
Let's not forget Node.js!
It's a backend server that uses Google Chrome's V8 JavaScript interpretor/compiler. And it runs JavaScript as a backend scripting engine.
You have access to filesystem, databases and everything if you use that (or any other backend system for that matter) and still be using JavaScript. You can use libraries too. Either written in JavaScript or libraries written in other languages that have been linked to interface with Node.js.
Edit 2:
There is a PC emulator written entirely in JavaScript. It runs binary executables if you want it to. It's called JSLinux.
If you're feeling particularly rambunctious you can grab the ffmpeg binary executable (compiled with static linking). And embed it into your application code as an uuencoded string then use JSLinux to execute the commands and grab the results.

Indeed, it is possible doing this on the client using the latest js technologies. A web-worker thread can do the work in the background. At least in Firefox and Chrome it is also possible to read ("upload in memory") and write ("download from memory") files using the new W3C File API, see here.
I managed to read files via drag&drop from and within the client using google's GWT which in the end is plain javascript, so it must also be possible to do it "natively".
Besides that, the conversation algorithm of course has to be implemented in a javascript web worker to avoid blocking the gui. This should be the hardest part, but not impossible, though.

You would need a backend to do this. You may want to look into the PHPExtension of FFmpeg

work on the files in a directory using html javascript

Trying to see if this is possible -
1.) User logs into our site
2.) Points to a directory
3.) The javascript code reads contents of the directory, shows thumbnails for any jpeg/gif in those directories. This all without uploading all the photos to the server. Kind of a semi desktop app.
Point 3 is something I have never done, is this possible for an online application to do ?

You can't do this...yet (unless you're using a prerelease of Chrome 9). There are some APIs coming down the pike that will make this possible in browsers that support them; there's a description of using them in this article.
But right now, no. To do this, you'll need to use a technology that allows local file access, such as a signed Java applet (normal unsigned ones obviously can't do this) or, on a severely limited number of platforms and browsers, an ActiveX control.
Update: Sorry, the new JavaScript APIs I mentioned above don't give you (user-granted) access to any old directory on their system. They do give you access to the file system, but it's a sandboxed file system. So you'd have to have the users move the files into the sandbox (which you could do via the File API and with drag-and-drop, keeping it an entirely client-side thing, no uploading required). But that isn't quite what you described.

No; this is not possible.
Javascript cannot directly interact with the user's local filesystem

No, it is not possible to access any of the clients files using JavaScript as that would be a security risk.