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DOKY-190 Extract persistence logic to separate submodule (#129)
Add submodule `persistence` to hold interaction with database. Make other submodules depend on it. Important! Extracting persistence layer leads to align dependency version to be aligned and make dependency management more centralized. Refactor dependencies and remove unused files Reorganized dependency management with a `libs.versions.toml` file and streamlined Gradle configurations across modules. Removed obsolete files, including unused tests, entities, properties, and services, to clean up the codebase. This improves maintainability and aligns with best practices for modular development. Centralized Flyway migration scripts into the `persistence` module. Adjusted Flyway configuration paths in application properties files and unified plugin application in the root Gradle file to streamline build configurations, removed unnecessary Gradle wrapper files.
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