If you haven't had a response yet.
Add the files in the tsconfig.json. It fixed my issue. My application-base-js is in a custom folder at the moment due to a code base issue with npm
"include": [
"./src/**/*"
],
"exclude": [
"./node_modules",
"./tsrules"
],
"files": [
"./node_modules/@types/arcgis-js-api/index.d.ts",
"./node_modules/dojo-typings/dojo/1.11/loader.d.ts",
"./node_modules/dojo-typings/dojo/1.11/index.d.ts",
"./node_modules/dojo-typings/dojo/1.11/modules.d.ts",
"./node_modules/dojo-typings/dijit/1.11/index.d.ts",
"./node_modules/dojo-typings/dijit/1.11/modules.d.ts",
"./node_modules/dojo-typings/dojox/1.11/index.d.ts",
"./node_modules/dojo-typings/dojox/1.11/modules.d.ts",
"./src/libs/@esri/application-base-js/support/updates.d.ts",
"./src/libs/@esri/application-base-js/support/updates.d.ts",
"./src/libs/@esri/application-base-js/index.d.ts",
"./src/libs/@esri/application-base-js/interfaces.d.ts"
]