@ryan cavanaugh

thanks for taking a look, I think I can demonstrate some problems

you can build this project with

$ tsc --project tsconfig-amd.json
$ tsc --project tsconfig-system.json

These two different configs are identical except one targets AMD the other targets SystemJS. The short of this, is:

1. that AMD transpiles correctly, but SystemJS does not.
2. With either AMD or SystemJS, only 12 of my 100+ .js/.ts files get included in the bundle, not sure why

You will notice in either the dist/systemjs-bundle.js file or dist/amd-bundle.js file, that there are only 12 System.register calls (try ctrl+f)

However, my lib directory has many more like 100+ .ts/.js files

so the first problem (1) is that TSC is not picking up all my files, not sure why
the second problem (2) is that TSC is not taking my modules and accurately transpiling them.

For example, an original .ts module looks like this:

'use strict';

//polyfills
const process = require('suman-browser-polyfills/modules/process');
const global = require('suman-browser-polyfills/modules/global');

//core
const domain = require('domain');
const util = require('util');

//npm
const pragmatik = require('pragmatik');
const async = require('async');
const colors = require('colors/safe');

//project
const _suman = global.__suman = (global.__suman || {});
const rules = require('../helpers/handle-varargs');
const constants = require('../../config/suman-constants');
const handleSetupComplete = require('../handle-setup-complete');

///////////////////////////////////////////////////////////////////////////////////////

function handleBadOptions(opts: IAfterOpts): void {

    if (opts.plan !== undefined && !Number.isInteger(opts.plan)) {
        console.error(' => Suman usage error => "plan" option is not an integer.');
        process.exit(constants.EXIT_CODES.OPTS_PLAN_NOT_AN_INTEGER);
        return;
    }
}

//////////////////////////// inline types  ///////////////////////////////////

//TODO

////////////////////////////////////////////////////////////////////////////

export = function (suman: ISuman, zuite: ITestSuite): Function {

    return function ($desc: string, $opts: IAfterOpts, $fn: Function): ITestSuite {

        handleSetupComplete(zuite);

        const args: Array<any> = pragmatik.parse(arguments, rules.hookSignature, {
            preParsed: typeof $opts === 'object' ? $opts.__preParsed : null
        });

        // this transpiles much more nicely, rather than inlining it above
        const [desc, opts, fn] = args;
        handleBadOptions(opts);

        if (opts.skip) {
            suman.numHooksSkipped++;
        }
        else if (!fn) {
            suman.numHooksStubbed++;
        }
        else {
            zuite.getAfters().push({
                ctx: zuite,
                timeout: opts.timeout || 11000,
                desc: desc || (fn ? fn.name : '(unknown due to stubbed function)'),
                cb: opts.cb || false,
                throws: opts.throws,
                planCountExpected: opts.plan,
                fatal: !(opts.fatal === false),
                fn: fn,
                type: 'after/teardown',
                warningErr: new Error('SUMAN_TEMP_WARNING_ERROR')
            });
        }

        return zuite;

    };


};

but the transpiled module looks like this:

System.register("test-suite-methods/make-after", [], function (exports_7, context_7) {
    'use strict';
    var __moduleName = context_7 && context_7.id;
    function handleBadOptions(opts) {
        if (opts.plan !== undefined && !Number.isInteger(opts.plan)) {
            console.error(' => Suman usage error => "plan" option is not an integer.');
            process.exit(constants.EXIT_CODES.OPTS_PLAN_NOT_AN_INTEGER);
            return;
        }
    }
    var process, global, domain, util, pragmatik, async, colors, _suman, rules, constants, handleSetupComplete;
    return {
        setters: [],
        execute: function () {
            process = require('suman-browser-polyfills/modules/process');
            global = require('suman-browser-polyfills/modules/global');
            domain = require('domain');
            util = require('util');
            pragmatik = require('pragmatik');
            async = require('async');
            colors = require('colors/safe');
            _suman = global.__suman = (global.__suman || {});
            rules = require('../helpers/handle-varargs');
            constants = require('../../config/suman-constants');
            handleSetupComplete = require('../handle-setup-complete');
        }
    };
});

Here are my hypotheses:

1. TSC is (erroneously) not including .js files at all (only is transpiling .ts files, and moving those to --outFile) (seems likely)
2. I do not currently have a hypothesis WRT why SystemJS is not being transpiled accurately. AMD seems to be OK.

As an aside, I would like to be able to bundle everything, including node_modules, that is a whole other challenge I think. Any advice regarding that would be much appreciated.