JavaScript file not updated after typescript file change

I have a .net core app with angular and all was working. I haven't touch the js end for 4 weeks while I worked on the .net. This also involved updating some npm packages etc.

Now I find that the main.js is not getting changed and reason being is that the ts-js link seems to have disappeared. e.g Changes to a ts file (or even creating a new one) does not generate a corresponding js file like it should.

Webpack cmd runs ok. Build in VS 2017 runs ok.

My tsconfig.json

   {
 "compilerOptions": {
"moduleResolution": "node",
"target": "es5",
"sourceMap": true,
"experimentalDecorators": true,
"emitDecoratorMetadata": true,
"skipDefaultLibCheck": true,
"lib": [ "es6", "dom" ],
"types": [ "node" ]

 },

 "exclude": [ "bin", "node_modules" ],
 "atom": { "rewriteTsconfig": false }
}

My webpack.config.js

 const path = require('path');
const webpack = require('webpack');
const merge = require('webpack-merge');
const CheckerPlugin = require('awesome-typescript-loader').CheckerPlugin;

module.exports = (env) => {
    // Configuration in common to both client-side and server-side bundles
    const isDevBuild = !(env && env.prod);
    const sharedConfig = {
        stats: { modules: false },
        context: __dirname,
        resolve: { extensions: [ '.js', '.ts' ] },
        output: {
            filename: '[name].js',
            publicPath: '/dist/' // Webpack dev middleware, if enabled, handles requests for this URL prefix
        },
        module: {
            rules: [
                { test: /\.ts$/, include: /ClientApp/, use: ['awesome-typescript-loader?silent=true', 'angular2-template-loader'] },
                { test: /\.html$/, use: 'html-loader?minimize=false' },
                { test: /\.css$/, use: [ 'to-string-loader', isDevBuild ? 'css-loader' : 'css-loader?minimize' ] },
                { test: /\.(png|jpg|jpeg|gif|svg)$/, use: 'url-loader?limit=25000' }
            ]
        },
        plugins: [
            new CheckerPlugin(),
            new webpack.ProvidePlugin({ $: 'jquery', jQuery: 'jquery' }),
        ]
    };

    // Configuration for client-side bundle suitable for running in browsers
    const clientBundleOutputDir = './wwwroot/dist';
    const clientBundleConfig = merge(sharedConfig, {
        entry: { 'main-client': './ClientApp/boot-client.ts' },
        output: { path: path.join(__dirname, clientBundleOutputDir) },
        plugins: [
            new webpack.DllReferencePlugin({
                context: __dirname,
                manifest: require('./wwwroot/dist/vendor-manifest.json')
            })
        ].concat(isDevBuild ? [
            // Plugins that apply in development builds only
            new webpack.SourceMapDevToolPlugin({
                filename: '[file].map', // Remove this line if you prefer inline source maps
                moduleFilenameTemplate: path.relative(clientBundleOutputDir, '[resourcePath]') // Point sourcemap entries to the original file locations on disk
            })
        ] : [
            // Plugins that apply in production builds only
            new webpack.optimize.UglifyJsPlugin()
        ])
    });

    // Configuration for server-side (prerendering) bundle suitable for running in Node
    const serverBundleConfig = merge(sharedConfig, {
        resolve: { mainFields: ['main'] },
        entry: { 'main-server': './ClientApp/boot-server.ts' },
        plugins: [
            new webpack.DllReferencePlugin({
                context: __dirname,
                manifest: require('./ClientApp/dist/vendor-manifest.json'),
                sourceType: 'commonjs2',
                name: './vendor'
            })
        ],
        output: {
            libraryTarget: 'commonjs',
            path: path.join(__dirname, './ClientApp/dist')
        },
        target: 'node',
        devtool: 'inline-source-map'
    });

    return [clientBundleConfig, serverBundleConfig];
};

My webpack.config.vendor.js

   const path = require('path');
const webpack = require('webpack');
const ExtractTextPlugin = require('extract-text-webpack-plugin');
const merge = require('webpack-merge');

module.exports = (env) => {
    const extractCSS = new ExtractTextPlugin('vendor.css');
    const isDevBuild = !(env && env.prod);
    const sharedConfig = {
        stats: { modules: false },
        resolve: { extensions: [ '.js' ] },
        module: {
            rules: [
                { test: /\.(png|woff|woff2|eot|ttf|svg)(\?|$)/, use: 'url-loader?limit=100000' }
            ]
        },
        entry: {
            vendor: [
                '@angular/animations',
                '@angular/common',
                '@angular/compiler',
                '@angular/core',
                '@angular/forms',
                '@angular/http',
                '@angular/platform-browser',
                '@angular/platform-browser-dynamic',
                '@angular/router',
                'bootstrap',
                'bootstrap/dist/css/bootstrap.css',
                'es6-shim',
                'es6-promise',

                'event-source-polyfill',
                'jquery',
                'zone.js',
            ]
        },
        output: {
            publicPath: '/dist/',
            filename: '[name].js',
            library: '[name]_[hash]'
        },
        plugins: [
            new webpack.ProvidePlugin({ $: 'jquery', jQuery: 'jquery' }), // Maps these identifiers to the jQuery package (because Bootstrap expects it to be a global variable)
            new webpack.ContextReplacementPlugin(/\@angular\b.*\b(bundles|linker)/, path.join(__dirname, './ClientApp')), // Workaround for https://github.com/angular/angular/issues/11580
            new webpack.ContextReplacementPlugin(/angular(\\|\/)core(\\|\/)@angular/, path.join(__dirname, './ClientApp')), // Workaround for https://github.com/angular/angular/issues/14898
            new webpack.IgnorePlugin(/^vertx$/) // Workaround for https://github.com/stefanpenner/es6-promise/issues/100
        ]
    };

    const clientBundleConfig = merge(sharedConfig, {
        output: { path: path.join(__dirname, 'wwwroot', 'dist') },
        module: {
            rules: [
                { test: /\.css(\?|$)/, use: extractCSS.extract({ use: isDevBuild ? 'css-loader' : 'css-loader?minimize' }) },
                { test: require.resolve('jquery'), loader: 'expose-loader?jQuery!expose-loader?$' }
            ]
        },
        plugins: [
            extractCSS,
            new webpack.DllPlugin({
                path: path.join(__dirname, 'wwwroot', 'dist', '[name]-manifest.json'),
                name: '[name]_[hash]'
            })
        ].concat(isDevBuild ? [] : [
            new webpack.optimize.UglifyJsPlugin()
        ])
    });

    const serverBundleConfig = merge(sharedConfig, {
        target: 'node',
        resolve: { mainFields: ['main'] },
        output: {
            path: path.join(__dirname, 'ClientApp', 'dist'),
            libraryTarget: 'commonjs2',
        },
        module: {
            rules: [
                { test: /\.css(\?|$)/, use: ['to-string-loader', isDevBuild ? 'css-loader' : 'css-loader?minimize'] }
                 //Gary Aadded
                ,{ test: require.resolve('jquery'), loader: 'expose-loader?jQuery!expose-loader?$' }

            ]

        },
        entry: { vendor: ['aspnet-prerendering'] },
        plugins: [
            new webpack.DllPlugin({
                path: path.join(__dirname, 'ClientApp', 'dist', '[name]-manifest.json'),
                name: '[name]_[hash]'
            })
        ]
    });

    return [clientBundleConfig, serverBundleConfig];
}

No one seems to actually know how this stuff works as there is usually 100 theories as to the problem but rarely a solution but here's hoping.