Add fix index mismatch flag into examples
The latest version of Acorn does not fix the indexing mis-match that appears from Athena, by default - it needs to be turned on manually. This is done in the CTD2023 example, but not yet in Example 1 & 2. This is okay, since the update is only in AthenaRootReader. In general, we should do the following:
- Remove AthenaReader as deprecated
- Make ROOT reading the default approach
- Make all examples available with the ROOT reader approach