Visual Studio 2015 compiles ALL typescript files when SINGLE file is changed

Try "ECMAScript 5" instead of "ECMAScript 3" in "ECMAScript version

I had a similar issue, but since we were handling TS compilation on our own, I wanted to avoid auto-compilation at all...

The fix was to force the TypeScriptCompileOnSaveEnabled flag to false inside the project:

<PropertyGroup>
    <TypeScriptCompileOnSaveEnabled>false</TypeScriptCompileOnSaveEnabled>
</PropertyGroup>

in my case this effectively stopped VS2015 from automatically compiling the .ts files on save, without VS getting into the way every time and messing up outputs...

Another work around: You could use Gulp to generate your compiled js files and maps. With Gulp you can also create a watch task to compile at a save of a ts file. You can even create clean tasks to clean up the project.

Example of a build task:

var tsProject = ts.createProject(paths.typescriptRoot + 'tsConfig.json'); // use tsconfig.json
    gulp.task("tsbuild", function () {
        var tsResult = tsProject.src()
            .pipe(sourcemaps.init()) // needed to create sourcemaps
            .pipe(ts(tsProject)); // use tsconfig.json
        return tsResult.js
            .pipe(concat(paths.concatTsFileName)) // concat all output files into a sings js files
            .pipe(sourcemaps.write()) // write the sourcemap to be able to debug the ts files
            .pipe(gulp.dest(paths.typescriptOut)); // output the result on specific path
    });

Example of a cleanup task :

gulp.task("clean:tsout", function (cb) {
    rimraf(paths.typescriptOut + paths.concatTsFileName, cb); // rimraf is used to delete a folder
});

gulp.task("clean:scriptjs",
    function () {
        return gulp.src(paths.typescriptJs, { read: false })  // to clean up multiple files we need to use gulp-rimraf
          .pipe(gulpRimraf());
    });

Example of a Watch task:

gulp.task("watch:tsbuild", ['tsbuild'], function () {
    gulp.watch(paths.typescriptRoot + '**/*.ts', ['tbbuild']);
});