Maybe this will help:

Select[VertexList[depgraph], 
 Context @@ MakeExpression[#, StandardForm] === "Global`" &]

Your definitions are probably in the Global context. This should filter out calls to built-in functions which are in the System or some other context. If your definitions are in some other context, you have to modify "Global`". If you don't know what the context is, execute Context[main], where main is your function in question. It will tell you the context of main.

I should say that I wouldn't want to go down the road of parsing your notebook. I'm sure it can be done. I could probably figure it out. Given enough hours. If the above doesn't filter out enough, try quitting the kernel and then executing the definitions in your notebook. Then the above should make the job feasible, unless you've loaded up your init.m with loads of other definitions.

Do you know about AutoGeneratePackage? Either code below will save the cells marked InitializationCell (see menu Cell > Cell Properties > Initialization Cell, shortcut ctrl-8):

SetOptions[EvaluationNotebook[], AutoGeneratedPackage -> Automatic]
SetOptions[EvaluationNotebook[], AutoGeneratedPackage -> Manual]

See the documentation for the difference between Automatic and Manual. You could also look at the code for GeneralUtilities`PrintDefinitions (via GeneralUtilities`PrintDefinitions[GeneralUtilities`PrintDefinitions]), which prints code to a notebook. It may take some work to figure it out, since it does a lot of pretty-print formatting with hyperlinks. It's much more complicated than the basic task you want to do.

Here's a usage string generator similar to what you want:

ClearAll[fff];
fff[x_, y_ : 2] := x + y;
fff[x_, y_, z_] := x  z + y;

fff::usage = StringJoin@ Riffle[ToString /@ HoldForm @@@ DownValues[fff][[All, 1]], "\n"];
? fff

A more complicated example:

ClearAll[fn];
fn[e_, {x_, a_, b_}][x0_?NumericQ] := Block[{x = x0}, e];
fn[e_, {x_, a_, b_}]["Domain"] := {x, a, b};
fn[e_, {x_, a_, b_}]["Variable"] := x;
fn[e_, x_Symbol] := fn[e, {x, 0, 1}]; (* default domain *)
fn /: Plot[f_fn] := 
  With[{x = f["Variable"], domain = f["Domain"]}, Plot[f[x], domain]];

fn::usage = StringJoin@ Riffle[
   ToString /@ HoldForm @@@ Join[UpValues[fn], SubValues[fn], DownValues[fn]][[All, 1]], 
    "\n"];

One could also just write a utility function to use on functions under development:

usage[symb_] := HoldForm @@@ 
    Join[UpValues[symb], SubValues[symb], DownValues[symb]][[All, 1]] // 
   Column;

Hello Michael, Thank you very much for the information.This solves this issue for me. Given that I can obtain the function tree of a particular function, I wonder if there is a tool that would be able to then automatically write the usage header in the package and then copy the actual function code into the package. For instance, I have function called getFinancialData[...] I would like the usage section of the package to be getFinancialData::usage = "getFinancialData[symbol,{startDate,endDate,period:'Day'}]."; And then have the definition for getFinancial package copied from the notebook to the package file. This would allow someone to write code, test it, improve functions, etc,,, Then, when satisfied that you have a properly running main function, put all the finally used functions in a package while leaving behind all the early attempts or those functions that fell by the wayside.