Thanks for reporting the issue.
I have reproduced such behavior even for standalone add-on project (not composite project). Changelogs from dependencies not being executed.
Invesigation of the issue shown that it is caused by Liquibase version upgrade in Jmix 2.0.
The problem can be solved by modifying includeAll tag in add-on root changelog.
<includeAll path="/com/company/core/liquibase/changelog"/>
should be changed to <includeAll path="/changelog" relativeToChangelogFile="true"/>
Changelog generation in Studio will be fixed in the next release, but for existing project this should be done manually.
Modify changelog.xml as per the method you suggested.
Test on the composite project.
Changelog scripts are generated successfully for add-ons.
However, an error occurs when recreating the DB for the main-app.
Starting Liquibase at 16:42:53 (version 4.20.0 #7837 built at 2023-03-07 16:25+0000)
[2023-08-09 16:42:54] INFO [liquibase.database] Set default schema name to PUBLIC
[2023-08-09 16:42:54] INFO [liquibase.changelog] Reading resource: com/company/core/liquibase/changelog/2023/07/24-142653-42234524.xml
[2023-08-09 16:42:54] INFO [liquibase.changelog] Reading resource: com/company/core/liquibase/changelog/2023/07/24-142653-42234524.xml
[2023-08-09 16:42:54] INFO [liquibase.changelog] Reading resource: com/company/organization/liquibase/changelog/2023/08/09-153809-42234524.xml
[2023-08-09 16:42:54] INFO [liquibase.changelog] Reading resource: com/company/main/liquibase/changelog/010-init-user.xml
[2023-08-09 16:42:54] INFO [liquibase.changelog] Change failed validation!
Unexpected error running Liquibase: Validation Failed:
1 changesets had duplicate identifiers
com/company/core/liquibase/changelog/2023/07/24-142653-42234524.xml::1::core
For more information, please use the --logLevel flag
[2023-08-09 16:42:55] SEVERE [liquibase.integration] Unexpected error running Liquibase: Validation Failed:
1 changesets had duplicate identifiers
com/company/core/liquibase/changelog/2023/07/24-142653-42234524.xml::1::core
liquibase.exception.ValidationFailedException: Validation Failed:
1 changesets had duplicate identifiers
com/company/core/liquibase/changelog/2023/07/24-142653-42234524.xml::1::core
at liquibase.changelog.DatabaseChangeLog.validate(DatabaseChangeLog.java:357)
at liquibase.Liquibase$16.run(Liquibase.java:2296)
at liquibase.Scope.lambda$child$0(Scope.java:187)
at liquibase.Scope.child(Scope.java:196)
at liquibase.Scope.child(Scope.java:186)
at liquibase.Scope.child(Scope.java:165)
at liquibase.Liquibase.runInScope(Liquibase.java:2639)
at liquibase.Liquibase.listUnrunChangeSets(Liquibase.java:2286)
at liquibase.Liquibase.isUpToDateFastCheck(Liquibase.java:506)
at liquibase.Liquibase.lambda$update$1(Liquibase.java:237)
at liquibase.Scope.lambda$child$0(Scope.java:187)
at liquibase.Scope.child(Scope.java:196)
at liquibase.Scope.child(Scope.java:186)
at liquibase.Scope.child(Scope.java:165)
at liquibase.Liquibase.runInScope(Liquibase.java:2639)
at liquibase.Liquibase.update(Liquibase.java:236)
at liquibase.Liquibase.update(Liquibase.java:221)
at liquibase.integration.commandline.Main.lambda$doMigration$1(Main.java:1757)
at liquibase.Scope.lambda$child$0(Scope.java:187)
at liquibase.Scope.child(Scope.java:196)
at liquibase.Scope.child(Scope.java:186)
at liquibase.Scope.child(Scope.java:165)
at liquibase.integration.commandline.Main.doMigration(Main.java:1756)
at liquibase.integration.commandline.Main$1.lambda$run$0(Main.java:415)
at liquibase.Scope.lambda$child$0(Scope.java:187)
at liquibase.Scope.child(Scope.java:196)
at liquibase.Scope.child(Scope.java:186)
at liquibase.Scope.child(Scope.java:165)
at liquibase.integration.commandline.Main$1.run(Main.java:414)
at liquibase.integration.commandline.Main$1.run(Main.java:231)
at liquibase.Scope.child(Scope.java:196)
at liquibase.Scope.child(Scope.java:172)
at liquibase.integration.commandline.Main.run(Main.java:231)
at liquibase.integration.commandline.Main.main(Main.java:173)
There is another issue from Liquibase when using includeAll tag in dependencies.
You get this “changesets had duplicate identifiers” if changelog.xml file from transitive dependency explicitly included to your main changelog.
E.g. for composite project above with core, organization add-ons and main app. If you have organization depending on core and main depending on organization adding core changelog to the main changelog.xml is not needed, because it will be added transitively from organization add-on. If added, the error you provided occurs.
Unfortunately Studio erroneously suggests to add this include. This will be fixed in the next release.
To fix the problem, check main app changelog and remove include of core add-on changelog.