are Passwords are not hard-coded into the application or stored in batch files ? regardless of hosting option .
For Server and Data Center, passwords are stored in the Jira database.
For Cloud, you'll have to ask Atlassian where passwords are stored for Atlassian accounts.
Actually, they are not.
Even for internal accounts, the passwords are not stored. If the server/DC is hooked up to an external user directory, they may be stored there (if it's a primitive one that doesn't do security properly)
Jira's internal user directory ("embedded crowd") stores only password hashes, not passwords.
Only one password might be found in a server/DC system files or database - if the database is configured with basic authentication, then the database user and password will be stored as plain text in <jira home>/dbconfig.xml
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