Building angular package results in: Cannot find module "jquery/index"

Question

I am developing an Angular module and after compiling and bundling it with ngc and rollup I am getting the following error in my Angular project:

Cannot find module "jquery/index"

In one of the module files I have the following import:

import * as jQuery from 'jquery';

In the module's UMD file the jquery import is declared as jquery/index. When I change it to jquery everything works as it should. However each time I rebuild and bundle the package I have to fix the problem again as rollup (or ngc) somehow changes the import from jquery to jquery/index.

So the main question is why the jquery import statement is changed after compiling and bundling?

My tsconfig:

{
"compilerOptions": {
    "declaration": true,
    "module": "es2015",
    "target": "es5",
    "baseUrl": ".",
    "stripInternal": true,
    "emitDecoratorMetadata": true,
    "experimentalDecorators": true,
    "allowSyntheticDefaultImports": true,
    "moduleResolution": "node",
    "outDir": "../build",
    "rootDir": ".",
    "lib": [
        "es2016",
        "dom"
    ],
    "skipLibCheck": true,
    "types": []
},
"angularCompilerOptions": {
    "annotateForClosureCompiler": true,
    "strictMetadataEmit": true,
    "skipTemplateCodegen": true,
    "flatModuleOutFile": "chassis-core.js",
    "flatModuleId": "chassis-core"
},
"files": [
    "./index.ts"
]
}