`composer require` fails because "Source directory docroot/core has uncommitted changes"
Explanation: The problem is that cweagans/composer-patches is applying patches to Drupal Core after cloning it, leading Composer to believe you've modified the affected files and therefore to prompt you to overwrite them lest you unwittingly lose work in progress.

Solution: Configure Composer to discard-changes which "[sets] the default style of handling dirty updates when in non-interactive mode... [to] always discard changes in vendors", then modify your script to pass the --no-interaction (or -n) flag. E.g.:

$ composer config discard-changes true
$ composer require -n drupal/examples
Using version 1.x-dev for drupal/examples
./composer.json has been updated
Gathering patches for root package.
Removing package drupal/core so that it can be re-installed and re-patched.
  - Removing drupal/core (8.6.x-dev)
Deleting docroot/core - deleted
Loading composer repositories with package information
Updating dependencies (including require-dev)
Package operations: 1 install, 0 updates, 0 removals
Gathering patches for root package.
No patches supplied.
Gathering patches for dependencies. This might take a minute.
  - Installing drupal/core (8.6.x-dev 8dbf42a): Cloning 8dbf42a90c from cache
  - Applying patches for drupal/core
    https://www.drupal.org/files/issues/2869592-remove-update-warning-7.patch (2869592 - Disabled update module shouldn't produce a status report warning)
    https://www.drupal.org/files/issues/2885441-2.patch (2885441 - EntityReferenceAutocompleteWidget should define its size setting as an integer)
    https://www.drupal.org/files/issues/2018-09-24/2815221-109.patch (2815221 - Add quickedit to the latest-revision route)
    https://www.drupal.org/files/issues/2018-10-12/1356276-531.patch (1356276 - Allow profiles to define a base/parent profile and load them in the correct order)
    https://www.drupal.org/files/issues/2018-07-09/2914389-8-do-not-test.patch (2914389 - Allow profiles to exclude dependencies of their parent)

Writing lock file
Generating autoload files