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Fix dependabot execution #1991

@jbonofre

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@jbonofre

Today, even if dependabot is enabled, the daily execution fails with the following error:

updater | 2025/08/29 20:20:58 ERROR <job_1087021425> Error during file fetching; aborting: Is a directory @ io_fread - /home/dependabot/dependabot-updater/repo/specs/java.xml
updater | 2025/08/29 20:20:58 ERROR <job_1087021425> Is a directory @ io_fread - /home/dependabot/dependabot-updater/repo/specs/java.xml
updater | 2025/08/29 20:20:58 ERROR <job_1087021425> /home/dependabot/common/lib/dependabot/file_fetchers/base.rb:235:in 'IO.read'
updater | 2025/08/29 20:20:58 ERROR <job_1087021425> /home/dependabot/common/lib/dependabot/file_fetchers/base.rb:235:in 'Dependabot::FileFetchers::Base#load_cloned_file_if_present'

It seems that a directory in the the source repository is considered as a file by dependabot. I will run locally and investigate.

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