File paths become relative after execution

[zhamidi]

I am trying to use tsickle-loader to transpile over 140 TypeScript files that are part of the same project into JS that I can later feed into Closure Compiler.
This is my webpack.config.js file:

const path = require("path");
const fs = require("fs");

const walkSync = function (dir, filelist) {
  const files = fs.readdirSync(dir);
  filelist = filelist || [];
  files.forEach(function (file) {
    if (fs.statSync(dir + file).isDirectory()) {
      filelist = walkSync(dir + file + "/", filelist);
    } else {
      filelist.push(dir + file);
    }
  });
  return filelist;
};

let input = walkSync("./src/", []).filter(f => f.endsWith(".ts") || f.endsWith(".json"));

module.exports = {
  entry: input,
  output: {
    path: path.resolve("./ts2compiler")
  },
  module: {
    rules: [
      {
        test: /\.ts$/,
        use: {
          loader: "tsickle-loader",
          options: {
            tsconfig: path.resolve(__dirname, "tsconfig.json"),
            externDir: "./ts2compiler"
          }
        }
      }
    ]
  }
};

The ẁalkSync function is to go through all the files that are in the different directories.
When I run the command ./node_modules/.bin/webpack --config webpack.config.js after a while I get the same error for all my files:

I tried both having my paths as absolute and relative in the entry property and it changes nothing.