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Does setTimeout get added to the call stack?

I've been learning about setTimeout and synchronous versus asynchronous code, I was watching a tutorial video where they showed various functions being called and added to the call stack, e.g. a function to simply add 2 numbers.
However for setTimeout they didn't show that when this was invoked that it was being added to the call stack, I understand that this fires up a web API and that the callback is added to a queue but I'm curious if in the moment that setTimeout is being executed by the JS engine, is it added to the call stack or not?

in the moment that setTimeout is being executed by the JS engine, is it added to the call stack or not?
It is. And it is popped from the call stack as soon as the callback is registered, so this hardly takes any time.
When the given delay has passed, the callback will be queued. Then when the call stack is empty, JS will process the event queue, and the callback will be called. Also this callback will be added to the call stack.
Just note that setTimeout and the callback will not be added to the call stack cumulative. It is guaranteed that the call stack will be emptied first before the callback will be pushed unto it.

Yes, after the time set in timeout passes, the callback is pushed to the call stack & executed.
Actually, the only way for a JS function to execute is to pass through the call stack.
Here is a good visualization tool called loupe by Philip Roberts that may help in understanding the call stack & things related to it.

setTimeout would be pushed to the call stack and then popped. When it is popped, it is sent to a browser API (if the code is executed in the browser). The API waits till the specified time is done and the callback is sent to the event queue. When the call stack is empty, the event loop will take the callback from the event queue (assuming it was next in line in the queue) and put it to the stack when it then gets executed.

Javascript event loop clarification

I keep seeing explanations of the "Javascript Event Loop" (ie: browser JS runtime event loop) that don't seem plausible to me, and I'm hoping someone can provide some authoritative clarification.
My base asssumption is that the JS event loop is just like event loops we've been working with in UI frameworks for decades, something like:
// [... some initialization ...]
// The Event Loop
while (true) {
if (! EventQueue.isEmpty()) {
event = EventQueue.pop_oldest_item();
event.callback(event [or some other kind of args]);
}
// [... defer to other non-JS tasks...]
}
But I keep seeing explanations (see below for examples) like this:
The event loop:
Checks whether the (Javascript) call stack is empty.
Checks whether the callback queue [AKA EventQueue] is empty.
If call stack is empty and callback queue is NOT empty, then:
a. Dequeue oldest callback queue item.
b. Push that callback function onto the call stack (and no mention is made of calling that function.)
Keep looping.
This obviously vaguely follows my assumed model above, but with two key and troubling differences:
A. Why would the event loop need to check that that the JS call stack is empty? Surely every time around the loop the call stack will be in the same state (whether that's completely "empty" is beside the point -- it doesn't need "checking"). Whatever function was called last time around will have returned, restoring the stack. So that part makes no sense.
B. Why would the event loop "push the callback onto the JS stack"? Shouldn't the event loop just call the function, thereby creating a legitimate stack frame, and a way to return from the function, not to mention actually executing the function?
So I would appreciate a clarification that addresses these explanations and why they are actually correct, or bolsters my strong suspicion that they are incorrect.
Example sources of these event loop explanations:
Philip Roberts: What the heck is the event loop anyway? At 14:00
https://youtu.be/8aGhZQkoFbQ?t=839
Typescript High Performance (book) page 83.
What is the Javascript event loop?
http://altitudelabs.com/blog/what-is-the-javascript-event-loop/
Understanding Javascript Function Executions - Call Stack, Event Loop, Tasks & more
https://medium.com/#gaurav.pandvia/understanding-javascript-function-executions-tasks-event-loop-call-stack-more-part-1-5683dea1f5ec

This is my answer to your question:
JavaScript behaves in a single threaded and synchronous manner, so the event callback function will be executed after Global Execution Context pops off the execution stack. All the event will be added into the what called event queue.
After global execution context finish all the execution, JS engine will keep checking if there exist any event inside the event queue. If JS engine sees there is an event, then it will create a new execution context for callback function and push it on the execution stack.
In JS, each time you invoke a function, JS engine will create an execute context, which creates a private scope where anything declared inside of the function can not be directly accessed from outside the current function scope, and pushes on the top of the execution context stack. After the function finish executing, the execution context will be popped off.

Because of the asynchronous nature of some functions that are executed in the call stack (event handlers, setTimeout, http requests) messages (callbacks) from these operations can be added to the message queue at any time. This can happen while the main thread is still running functions in the call stack so the event loop needs to check to see if it is empty or not. Once empty then it will pull the next message from the message queue and throw it into the call stack. This cycle constitutes the essence of the event loop.
I made a video presentation that explains and demonstrates this process:
https://www.youtube.com/watch?v=4xsvn6VUTwQ

Does the JS callstack always have at least one frame?

I've recently seen a presentation on the JS event loop which is, frankly, brilliant, but I have a lingering question now about the JS call stack. If you think about the global execution context as, say, main(), is main() never resolved? My reasoning here is that, if it were, then the JS program would be complete, and no callbacks would happen.
--edit
My primary interest here is how the call stack is represented, in relation to the callback queue. If the event loop is said to wait until the call stack is empty before pushing new frames onto the stack, then the loop would be waiting until the program is complete, and callbacks wouldn't have any effect.
I suppose that means that the event loop waits until there is only one frame left (the main execution context), not no frames.

If you think about the global execution context as, say, main()
No. main is not the global execution context, it is the code that initially runs in that context. The global environment is - through closure - still preserved for the outstanding callbacks after your global code ran, it will not get garbage-collected until your program has finished.
is main() never resolved?
Of course it is. main() is the invocation of any global code - basically, when you loaded a script in your webpage and it executes (yes, this can happen multiple times). Or the global program that you tell node to execute. And once that code has finished running, it does indeed get popped of the stack, as you can see in the talks's animation very well. It does not "continue to run", as that would block the event loop.
My reasoning here is that, if it were, then the JS program would be complete, and no callbacks would happen.
No. The script might have been completed, yes, but your program (browser environment, node etc) has not yet. The event loop is still spinning (or, to be exact: just starts spinning).
The event loop will look at the ongoing asynchronous tasks (XHRs, timeouts, file IO etc) and notice there still are some things working. The program does not exit. Once one (or multiple) of those tasks finish, they put their callback in the callback queue, where it gets picked up by the event loop, and processed by executing it on a brand new call stack. When that stack is empty again, the event loop is back in control, and picks up callbacks from the queue until it is empty. Then again, it looks whether there are still ongoing tasks (one of the callbacks might have spawned new ones), and only when there are none, then the program really ends, and the global environment can be trashed.
So yes, there are indeed times in the execution of a javascript program where the callstack is empty, and only the event loop is spinning happily - actually, that's the situation most of the time.

As you said, main() is the global execution context. It's still alive until :
you close the tab if you're in a browser
you kill the process if you're on a server (like node)
the tab/process crashes
So unless one of the use cases above happen, the runtime is still alive, so is the event loop (which will process the task queue).

Understanding the Event Loop

I am thinking about it and this is what I came up with:
Let's see this code below:
console.clear();
console.log("a");
setTimeout(function(){console.log("b");},1000);
console.log("c");
setTimeout(function(){console.log("d");},0);
A request comes in, and JS engine starts executing the code above step by step. The first two calls are sync calls. But when it comes to setTimeout method, it becomes an async execution. But JS immediately returns from it and continue executing, which is called Non-Blocking or Async. And it continues working on other etc.
The results of this execution is the following:
a c d b
So basically the second setTimeout got finished first and its callback function gets executed earlier than the first one and that makes sense.
We are talking about single-threaded application here. JS Engine keeps executing this and unless it finishes the first request, it won't go to second one. But the good thing is that it won't wait for blocking operations like setTimeout to resolve so it will be faster because it accepts the new incoming requests.
But my questions arise around the following items:
#1: If we are talking about a single-threaded application, then what mechanism processes setTimeouts while the JS engine accepts more requests and executes them? How does the single thread continue working on other requests? What works on setTimeout while other requests keep coming in and get executed.
#2: If these setTimeout functions get executed behind the scenes while more requests are coming in and being executed, what carries out the async executions behind the scenes? What is this thing that we talk about called the EventLoop?
#3: But shouldn't the whole method be put in the EventLoop so that the whole thing gets executed and the callback method gets called? This is what I understand when talking about callback functions:
function downloadFile(filePath, callback)
{
blah.downloadFile(filePath);
callback();
}
But in this case, how does the JS Engine know if it is an async function so that it can put the callback in the EventLoop? Perhaps something like the async keyword in C# or some sort of an attribute which indicates the method JS Engine will take on is an async method and should be treated accordingly.
#4: But an article says quite contrary to what I was guessing on how things might be working:
The Event Loop is a queue of callback functions. When an async
function executes, the callback function is pushed into the queue. The
JavaScript engine doesn't start processing the event loop until the
code after an async function has executed.
#5: And there is this image here which might be helpful but the first explanation in the image is saying exactly the same thing mentioned in question number 4:
So my question here is to get some clarifications about the items listed above?

1: If we are talking about a single-threaded application, then what processes setTimeouts while JS engine accepts more requests and executes them? Isn't that single thread will continue working on other requests? Then who is going to keep working on setTimeout while other requests keep coming and get executed.
There's only 1 thread in the node process that will actually execute your program's JavaScript. However, within node itself, there are actually several threads handling operation of the event loop mechanism, and this includes a pool of IO threads and a handful of others. The key is the number of these threads does not correspond to the number of concurrent connections being handled like they would in a thread-per-connection concurrency model.
Now about "executing setTimeouts", when you invoke setTimeout, all node does is basically update a data structure of functions to be executed at a time in the future. It basically has a bunch of queues of stuff that needs doing and every "tick" of the event loop it selects one, removes it from the queue, and runs it.
A key thing to understand is that node relies on the OS for most of the heavy lifting. So incoming network requests are actually tracked by the OS itself and when node is ready to handle one it just uses a system call to ask the OS for a network request with data ready to be processed. So much of the IO "work" node does is either "Hey OS, got a network connection with data ready to read?" or "Hey OS, any of my outstanding filesystem calls have data ready?". Based upon its internal algorithm and event loop engine design, node will select one "tick" of JavaScript to execute, run it, then repeat the process all over again. That's what is meant by the event loop. Node is basically at all times determining "what's the next little bit of JavaScript I should run?", then running it. This factors in which IO the OS has completed, and things that have been queued up in JavaScript via calls to setTimeout or process.nextTick.
2: If these setTimeout will get executed behind the scenes while more requests are coming and in and being executed, the thing carry out the async executions behind the scenes is that the one we are talking about EventLoop?
No JavaScript gets executed behind the scenes. All the JavaScript in your program runs front and center, one at a time. What happens behind the scenes is the OS handles IO and node waits for that to be ready and node manages its queue of javascript waiting to execute.
3: How can JS Engine know if it is an async function so that it can put it in the EventLoop?
There is a fixed set of functions in node core that are async because they make system calls and node knows which these are because they have to call the OS or C++. Basically all network and filesystem IO as well as child process interactions will be asynchronous and the ONLY way JavaScript can get node to run something asynchronously is by invoking one of the async functions provided by the node core library. Even if you are using an npm package that defines it's own API, in order to yield the event loop, eventually that npm package's code will call one of node core's async functions and that's when node knows the tick is complete and it can start the event loop algorithm again.
4 The Event Loop is a queue of callback functions. When an async function executes, the callback function is pushed into the queue. The JavaScript engine doesn't start processing the event loop until the code after an async function has executed.
Yes, this is true, but it's misleading. The key thing is the normal pattern is:
//Let's say this code is running in tick 1
fs.readFile("/home/barney/colors.txt", function (error, data) {
//The code inside this callback function will absolutely NOT run in tick 1
//It will run in some tick >= 2
});
//This code will absolutely also run in tick 1
//HOWEVER, typically there's not much else to do here,
//so at some point soon after queueing up some async IO, this tick
//will have nothing useful to do so it will just end because the IO result
//is necessary before anything useful can be done
So yes, you could totally block the event loop by just counting Fibonacci numbers synchronously all in memory all in the same tick, and yes that would totally freeze up your program. It's cooperative concurrency. Every tick of JavaScript must yield the event loop within some reasonable amount of time or the overall architecture fails.

Don't think the host process to be single-threaded, they are not. What is single-threaded is the portion of the host process that execute your javascript code.
Except for background workers, but these complicate the scenario...
So, all your js code run in the same thread, and there's no possibility that you get two different portions of your js code to run concurrently (so, you get not concurrency nigthmare to manage).
The js code that is executing is the last code that the host process picked up from the event loop.
In your code you can basically do two things: run synchronous instructions, and schedule functions to be executed in future, when some events happens.
Here is my mental representation (beware: it's just that, I don't know the browser implementation details!) of your example code:
console.clear(); //exec sync
console.log("a"); //exec sync
setTimeout( //schedule inAWhile to be executed at now +1 s
function inAWhile(){
console.log("b");
},1000);
console.log("c"); //exec sync
setTimeout(
function justNow(){ //schedule justNow to be executed just now
console.log("d");
},0);
While your code is running, another thread in the host process keep track of all system events that are occurring (clicks on UI, files read, networks packets received etc.)
When your code completes, it is removed from the event loop, and the host process return to checking it, to see if there are more code to run. The event loop contains two event handler more: one to be executed now (the justNow function), and another within a second (the inAWhile function).
The host process now try to match all events happened to see if there handlers registered for them.
It found that the event that justNow is waiting for has happened, so it start to run its code. When justNow function exit, it check the event loop another time, searhcing for handlers on events. Supposing that 1 s has passed, it run the inAWhile function, and so on....

The Event Loop has one simple job - to monitor the Call Stack, the Callback Queue and Micro task queue. If the Call Stack is empty, the Event Loop will take the first event from the micro task queue then from the callback queue and will push it to the Call Stack, which effectively runs it. Such an iteration is called a tick in the Event Loop.
As most developers know, that Javascript is single threaded, means two statements in javascript can not be executed in parallel which is correct. Execution happens line by line, which means each javascript statements are synchronous and blocking. But there is a way to run your code asynchronously, if you use setTimeout() function, a Web API given by the browser, which makes sure that your code executes after specified time (in millisecond).
Example:
console.log("Start");
setTimeout(function cbT(){
console.log("Set time out");
},5000);
fetch("http://developerstips.com/").then(function cbF(){
console.log("Call back from developerstips");
});
// Millions of line code
// for example it will take 10000 millisecond to execute
console.log("End");
setTimeout takes a callback function as first parameter, and time in millisecond as second parameter.
After the execution of above statement in browser console it will print
Start
End
Call back from developerstips
Set time out
Note: Your asynchronous code runs after all the synchronous code is done executing.
Understand How the code execution line by line
JS engine execute the 1st line and will print "Start" in console
In the 2nd line it sees the setTimeout function named cbT, and JS engine pushes the cbT function to callBack queue.
After this the pointer will directly jump to line no.7 and there it will see promise and JS engine push the cbF function to microtask queue.
Then it will execute Millions of line code and end it will print "End"
After the main thread end of execution the event loop will first check the micro task queue and then call back queue. In our case it takes cbF function from the micro task queue and pushes it into the call stack then it will pick cbT funcion from the call back queue and push into the call stack.

JavaScript is high-level, single-threaded language, interpreted language. This means that it needs an interpreter which converts the JS code to a machine code. interpreter means engine. V8 engines for chrome and webkit for safari. Every engine contains memory, call stack, event loop, timer, web API, events, etc.
Event loop: microtasks and macrotasks
The event loop concept is very simple. There’s an endless loop, where the JavaScript engine waits for tasks, executes them and then sleeps, waiting for more tasks
Tasks are set – the engine handles them – then waits for more tasks (while sleeping and consuming close to zero CPU). It may happen that a task comes while the engine is busy, then it’s enqueued. The tasks form a queue, so-called “macrotask queue”
Microtasks come solely from our code. They are usually created by promises: an execution of .then/catch/finally handler becomes a microtask. Microtasks are used “under the cover” of await as well, as it’s another form of promise handling. Immediately after every macrotask, the engine executes all tasks from microtask queue, prior to running any other macrotasks or rendering or anything else.

When is JavaScript synchronous?

I have been under the impression for that JavaScript was always asynchronous. However, I have learned that there are situations where it is not (ie DOM manipulations). Is there a good reference anywhere about when it will be synchronous and when it will be asynchronous? Does jQuery affect this at all?

JavaScript is always synchronous and single-threaded. If you're executing a JavaScript block of code on a page then no other JavaScript on that page will currently be executed.
JavaScript is only asynchronous in the sense that it can make, for example, Ajax calls. The Ajax call will stop executing and other code will be able to execute until the call returns (successfully or otherwise), at which point the callback will run synchronously. No other code will be running at this point. It won't interrupt any other code that's currently running.
JavaScript timers operate with this same kind of callback.
Describing JavaScript as asynchronous is perhaps misleading. It's more accurate to say that JavaScript is synchronous and single-threaded with various callback mechanisms.
jQuery has an option on Ajax calls to make them synchronously (with the async: false option). Beginners might be tempted to use this incorrectly because it allows a more traditional programming model that one might be more used to. The reason it's problematic is that this option will block all JavaScript on the page until it finishes, including all event handlers and timers.

JavaScript is single threaded and has a synchronous execution model. Single threaded means that one command is being executed at a time. Synchronous means one at a time i.e. one line of code is being executed at time in order the code appears. So in JavaScript one thing is happening at a time.
Execution Context
The JavaScript engine interacts with other engines in the browser.
In the JavaScript execution stack there is global context at the bottom and then when we invoke functions the JavaScript engine creates new execution contexts for respective functions. When the called function exits its execution context is popped from the stack, and then next execution context is popped and so on...
For example
function abc()
{
console.log('abc');
}
function xyz()
{
abc()
console.log('xyz');
}
var one = 1;
xyz();
In the above code a global execution context will be created and in this context var one will be stored and its value will be 1... when the xyz() invocation is called then a new execution context will be created and if we had defined any variable in xyz function those variables would be stored in the execution context of xyz(). In the xyz function we invoke abc() and then the abc() execution context is created and put on the execution stack... Now when abc() finishes its context is popped from stack, then the xyz() context is popped from stack and then global context will be popped...
Now about asynchronous callbacks; asynchronous means more than one at a time.
Just like the execution stack there is the Event Queue. When we want to be notified about some event in the JavaScript engine we can listen to that event, and that event is placed on the queue. For example an Ajax request event, or HTTP request event.
Whenever the execution stack is empty, like shown in above code example, the JavaScript engine periodically looks at the event queue and sees if there is any event to be notified about. For example in the queue there were two events, an ajax request and a HTTP request. It also looks to see if there is a function which needs to be run on that event trigger... So the JavaScript engine is notified about the event and knows the respective function to execute on that event... So the JavaScript engine invokes the handler function, in the example case, e.g. AjaxHandler() will be invoked and like always when a function is invoked its execution context is placed on the execution context and now the function execution finishes and the event ajax request is also removed from the event queue... When AjaxHandler() finishes the execution stack is empty so the engine again looks at the event queue and runs the event handler function of HTTP request which was next in queue. It is important to remember that the event queue is processed only when execution stack is empty.
For example see the code below explaining the execution stack and event queue handling by Javascript engine.
function waitfunction() {
var a = 5000 + new Date().getTime();
while (new Date() < a){}
console.log('waitfunction() context will be popped after this line');
}
function clickHandler() {
console.log('click event handler...');
}
document.addEventListener('click', clickHandler);
waitfunction(); //a new context for this function is created and placed on the execution stack
console.log('global context will be popped after this line');
And
<html>
<head>
</head>
<body>
<script src="program.js"></script>
</body>
</html>
Now run the webpage and click on the page, and see the output on console. The output will be
waitfunction() context will be popped after this line
global context will be emptied after this line
click event handler...
The JavaScript engine is running the code synchronously as explained in the execution context portion, the browser is asynchronously putting things in event queue. So the functions which take a very long time to complete can interrupt event handling. Things happening in a browser like events are handled this way by JavaScript, if there is a listener supposed to run, the engine will run it when the execution stack is empty. And events are processed in the order they happen, so the asynchronous part is about what is happening outside the engine i.e. what should the engine do when those outside events happen.
So JavaScript is always synchronous.

JavaScript is single-threaded, and all the time you work on a normal synchronous code-flow execution.
Good examples of the asynchronous behavior that JavaScript can have are events (user interaction, Ajax request results, etc) and timers, basically actions that might happen at any time.
I would recommend you to give a look to the following article:
How JavaScript Timers Work
That article will help you to understand the single-threaded nature of JavaScript and how timers work internally and how asynchronous JavaScript execution works.

To someone who really understands how JS works this question might seem off, however most people who use JS do not have such a deep level of insight (and don't necessarily need it) and to them this is a fairly confusing point, I will try to answer from that perspective.
JS is synchronous in the way its code is executed. each line only runs after the line before it has completed and if that line calls a function after that is complete etc...
The main point of confusion arises from the fact that your browser is able to tell JS to execute more code at anytime (similar to how you can execute more JS code on a page from the console). As an example JS has Callback functions who's purpose is to allow JS to BEHAVE asynchronously so further parts of JS can run while waiting for a JS function that has been executed (I.E. a GET call) to return back an answer, JS will continue to run until the browser has an answer at that point the event loop (browser) will execute the JS code that calls the callback function.
Since the event loop (browser) can input more JS to be executed at any point in that sense JS is asynchronous (the primary things that will cause a browser to input JS code are timeouts, callbacks and events)
I hope this is clear enough to be helpful to somebody.

Definition
The term "asynchronous" can be used in slightly different meanings, resulting in seemingly conflicting answers here, while they are actually not. Wikipedia on Asynchrony has this definition:
Asynchrony, in computer programming, refers to the occurrence of events independent of the main program flow and ways to deal with such events. These may be "outside" events such as the arrival of signals, or actions instigated by a program that take place concurrently with program execution, without the program blocking to wait for results.
non-JavaScript code can queue such "outside" events to some of JavaScript's event queues. But that is as far as it goes.
No Preemption
There is no external interruption of running JavaScript code in order to execute some other JavaScript code in your script. Pieces of JavaScript are executed one after the other, and the order is determined by the order of events in each event queue, and the priority of those queues.
For instance, you can be absolutely sure that no other JavaScript (in the same script) will ever execute while the following piece of code is executing:
let a = [1, 4, 15, 7, 2];
let sum = 0;
for (let i = 0; i < a.length; i++) {
sum += a[i];
}
In other words, there is no preemption in JavaScript. Whatever may be in the event queues, the processing of those events will have to wait until such piece of code has ran to completion. The EcmaScript specification says in section 8.4 Jobs and Jobs Queues:
Execution of a Job can be initiated only when there is no running execution context and the execution context stack is empty.
Examples of Asynchrony
As others have already written, there are several situations where asynchrony comes into play in JavaScript, and it always involves an event queue, which can only result in JavaScript execution when there is no other JavaScript code executing:
setTimeout(): the agent (e.g. browser) will put an event in an event queue when the timeout has expired. The monitoring of the time and the placing of the event in the queue happens by non-JavaScript code, and so you could imagine this happens in parallel with the potential execution of some JavaScript code. But the callback provided to setTimeout can only execute when the currently executing JavaScript code has ran to completion and the appropriate event queue is being read.
fetch(): the agent will use OS functions to perform an HTTP request and monitor for any incoming response. Again, this non-JavaScript task may run in parallel with some JavaScript code that is still executing. But the promise resolution procedure, that will resolve the promise returned by fetch(), can only execute when the currently executing JavaScript has ran to completion.
requestAnimationFrame(): the browser's rendering engine (non-JavaScript) will place an event in the JavaScript queue when it is ready to perform a paint operation. When JavaScript event is processed the callback function is executed.
queueMicrotask(): immediately places an event in the microtask queue. The callback will be executed when the call stack is empty and that event is consumed.
There are many more examples, but all these functions are provided by the host environment, not by core EcmaScript. With core EcmaScript you can synchronously place an event in a Promise Job Queue with Promise.resolve().
Language Constructs
EcmaScript provides several language constructs to support the asynchrony pattern, such as yield, async, await. But let there be no mistake: no JavaScript code will be interrupted by an external event. The "interruption" that yield and await seem to provide is just a controlled, predefined way of returning from a function call and restoring its execution context later on, either by JS code (in the case of yield), or the event queue (in the case of await).
DOM event handling
When JavaScript code accesses the DOM API, this may in some cases make the DOM API trigger one or more synchronous notifications. And if your code has an event handler listening to that, it will be called.
This may come across as pre-emptive concurrency, but it is not: it is the JavaScript code that initiates the API call, and thus controls that the API can do some stuff, but this is just like a function call: once your event handler(s) return(s), the DOM API will eventually also return, and the original JavaScript code will continue after the API call it made.
In other cases the DOM API will just dispatch an event in the appropriate event queue, and JavaScript will pick it up once the call stack has been emptied.
See synchronous and asynchronous events

"I have been under the impression for that JavaScript was always
asynchronous"
You can use JavaScript in a synchronous way, or an asynchronous way. In fact JavaScript has really good asynchronous support. For example I might have code that requires a database request. I can then run other code, not dependent on that request, while I wait for that request to complete. This asynchronous coding is supported with promises, async/await, etc. But if you don't need a nice way to handle long waits then just use JS synchronously.
What do we mean by 'asynchronous'. Well it does not mean multi-threaded, but rather describes a non-dependent relationship. Check out this image from this popular answer:
A-Start ------------------------------------------ A-End
| B-Start -----------------------------------------|--- B-End
| | C-Start ------------------- C-End | |
| | | | | |
V V V V V V
1 thread->|<-A-|<--B---|<-C-|-A-|-C-|--A--|-B-|--C-->|---A---->|--B-->|
We see that a single threaded application can have async behavior. The work in function A is not dependent on function B completing, and so while function A began before function B, function A is able to complete at a later time and on the same thread.
So, just because JavaScript executes one command at a time, on a single thread, it does not then follow that JavaScript can only be used as a synchronous language.
"Is there a good reference anywhere about when it will be synchronous and when it will be asynchronous"
I'm wondering if this is the heart of your question. I take it that you mean how do you know if some code you are calling is async or sync. That is, will the rest of your code run off and do something while you wait for some result? Your first check should be the documentation for whichever library you are using. Node methods, for example, have clear names like readFileSync. If the documentation is no good there is a lot of help here on SO. EG:
How to know if a function is async?