I forgot to mention, this is an update from redmine42-4.2.5 with a clean install, just moved database.yml, settings.yml, and /files to the new folder, no plugins migrated yet.

The code quoted in the error message is not part of Redmine 5.1.3. You can get more information by appending --trace to your command. Depending on the source of your Redmine code, someone may have adapted it.

In any case, note that the config/settings.yml file is specific to the respective Redmine version and you must not edit or replace it with an old version. See RedmineUpgrade for complete upgrade instructions.

Thanks for the help!

The source is https://www.freshports.org/www/redmine51/

Code for the FreeBSD port is https://github.com/freebsd/freebsd-ports/tree/main/www/redmine51

A few files are patched for FreeBSD.

To test in isolation, I did a completely new install, fresh database, no modifications to configuration.yml and only the database.yml settings to connect to the new database (noting that MariaDB throws an error with either the transaction_isolation or the tx_isolation variable set. The only modifications to the as-shipped /redmine folder are the following database.yml configurations:

# Default setup is given for MySQL 5.7.7 or later.
# Examples for PostgreSQL, SQLite3 and SQL Server can be found at the end.
# Line indentation must be 2 spaces (no tabs).

production:
  adapter: mysql2
  database: redmine5t
  host: 10.3.69.183
  username: redmine5t
  password: "randompassword" 
  # Use "utf8" instead of "utfmb4" for MySQL prior to 5.7.7
  encoding: utf8mb4
  variables:
    # Recommended `transaction_isolation` for MySQL to avoid concurrency issues is
    # `READ-COMMITTED`.
    # In case of MySQL lower than 8, the variable name is `tx_isolation`.
    # See https://www.redmine.org/projects/redmine/wiki/MySQL_configuration
    # should be updated to "transaction_isolation" after db update (then test)
    # transaction_isolation: "tx_isolation" 

development:
  adapter: mysql2
  database: redmine_development
  host: localhost
  username: root
  password: "" 
  # Use "utf8" instead of "utfmb4" for MySQL prior to 5.7.7
  encoding: utf8mb4
  variables:
    transaction_isolation: "READ-COMMITTED" 

# Warning: The database defined as "test" will be erased and
# re-generated from your development database when you run "rake".
# Do not set this db to the same as development or production.
test:
  adapter: mysql2
  database: redmine_test
  host: localhost
  username: root
  password: "" 
  # Use "utf8" instead of "utfmb4" for MySQL prior to 5.7.7
  encoding: utf8mb4
  variables:
    transaction_isolation: "READ-COMMITTED" 

Then the following command sequence yields:

$ whoami
redmine
$ bundle config set --local without 'development test'
You are replacing the current local value of without, which is currently "development:test" 
$ bundle install
Bundle complete! 30 Gemfile dependencies, 75 gems now installed.
Gems in the groups 'development' and 'test' were not installed.
Use `bundle info [gemname]` to see where a bundled gem is installed.
$ RAILS_ENV=production bundle exec rake db:migrate --trace
** Invoke db:migrate (first_time)
** Invoke db:load_config (first_time)
** Invoke environment (first_time)
** Execute environment
** Execute db:load_config
** Execute db:migrate
rake aborted!
NoMethodError: undefined method `stringify_keys' for nil:NilClass (NoMethodError)

          variables = @config.fetch(:variables, {}).stringify_keys
                                                   ^^^^^^^^^^^^^^^
/usr/local/lib/ruby/gems/3.2/gems/activerecord-6.1.7.8/lib/active_record/connection_adapters/abstract_mysql_adapter.rb:744:in `configure_connection'
/usr/local/lib/ruby/gems/3.2/gems/activerecord-6.1.7.8/lib/active_record/connection_adapters/mysql2_adapter.rb:144:in `configure_connection'
/usr/local/lib/ruby/gems/3.2/gems/activerecord-6.1.7.8/lib/active_record/connection_adapters/mysql2_adapter.rb:53:in `initialize'
/usr/local/lib/ruby/gems/3.2/gems/activerecord-6.1.7.8/lib/active_record/connection_adapters/mysql2_adapter.rb:22:in `new'
/usr/local/lib/ruby/gems/3.2/gems/activerecord-6.1.7.8/lib/active_record/connection_adapters/mysql2_adapter.rb:22:in `mysql2_connection'
/usr/local/lib/ruby/gems/3.2/gems/activerecord-6.1.7.8/lib/active_record/connection_adapters/abstract/connection_pool.rb:882:in `public_send'
/usr/local/lib/ruby/gems/3.2/gems/activerecord-6.1.7.8/lib/active_record/connection_adapters/abstract/connection_pool.rb:882:in `new_connection'
/usr/local/lib/ruby/gems/3.2/gems/activerecord-6.1.7.8/lib/active_record/connection_adapters/abstract/connection_pool.rb:926:in `checkout_new_connection'
/usr/local/lib/ruby/gems/3.2/gems/activerecord-6.1.7.8/lib/active_record/connection_adapters/abstract/connection_pool.rb:905:in `try_to_checkout_new_connection'
/usr/local/lib/ruby/gems/3.2/gems/activerecord-6.1.7.8/lib/active_record/connection_adapters/abstract/connection_pool.rb:866:in `acquire_connection'
/usr/local/lib/ruby/gems/3.2/gems/activerecord-6.1.7.8/lib/active_record/connection_adapters/abstract/connection_pool.rb:588:in `checkout'
/usr/local/lib/ruby/gems/3.2/gems/activerecord-6.1.7.8/lib/active_record/connection_adapters/abstract/connection_pool.rb:428:in `connection'
/usr/local/lib/ruby/gems/3.2/gems/activerecord-6.1.7.8/lib/active_record/connection_adapters/abstract/connection_pool.rb:1128:in `retrieve_connection'
/usr/local/lib/ruby/gems/3.2/gems/activerecord-6.1.7.8/lib/active_record/connection_handling.rb:327:in `retrieve_connection'
/usr/local/lib/ruby/gems/3.2/gems/activerecord-6.1.7.8/lib/active_record/connection_handling.rb:283:in `connection'
/usr/local/lib/ruby/gems/3.2/gems/activerecord-6.1.7.8/lib/active_record/tasks/database_tasks.rb:237:in `migrate'
/usr/local/lib/ruby/gems/3.2/gems/activerecord-6.1.7.8/lib/active_record/railties/databases.rake:92:in `block (3 levels) in <top (required)>'
/usr/local/lib/ruby/gems/3.2/gems/activerecord-6.1.7.8/lib/active_record/railties/databases.rake:90:in `each'
/usr/local/lib/ruby/gems/3.2/gems/activerecord-6.1.7.8/lib/active_record/railties/databases.rake:90:in `block (2 levels) in <top (required)>'
/usr/local/lib/ruby/gems/3.2/gems/rake-13.2.1/lib/rake/task.rb:281:in `block in execute'
/usr/local/lib/ruby/gems/3.2/gems/rake-13.2.1/lib/rake/task.rb:281:in `each'
/usr/local/lib/ruby/gems/3.2/gems/rake-13.2.1/lib/rake/task.rb:281:in `execute'
/usr/local/lib/ruby/gems/3.2/gems/rake-13.2.1/lib/rake/task.rb:219:in `block in invoke_with_call_chain'
/usr/local/lib/ruby/gems/3.2/gems/rake-13.2.1/lib/rake/task.rb:199:in `synchronize'
/usr/local/lib/ruby/gems/3.2/gems/rake-13.2.1/lib/rake/task.rb:199:in `invoke_with_call_chain'
/usr/local/lib/ruby/gems/3.2/gems/rake-13.2.1/lib/rake/task.rb:188:in `invoke'
/usr/local/lib/ruby/gems/3.2/gems/rake-13.2.1/lib/rake/application.rb:188:in `invoke_task'
/usr/local/lib/ruby/gems/3.2/gems/rake-13.2.1/lib/rake/application.rb:138:in `block (2 levels) in top_level'
/usr/local/lib/ruby/gems/3.2/gems/rake-13.2.1/lib/rake/application.rb:138:in `each'
/usr/local/lib/ruby/gems/3.2/gems/rake-13.2.1/lib/rake/application.rb:138:in `block in top_level'
/usr/local/lib/ruby/gems/3.2/gems/rake-13.2.1/lib/rake/application.rb:147:in `run_with_threads'
/usr/local/lib/ruby/gems/3.2/gems/rake-13.2.1/lib/rake/application.rb:132:in `top_level'
/usr/local/lib/ruby/gems/3.2/gems/rake-13.2.1/lib/rake/application.rb:83:in `block in run'
/usr/local/lib/ruby/gems/3.2/gems/rake-13.2.1/lib/rake/application.rb:214:in `standard_exception_handling'
/usr/local/lib/ruby/gems/3.2/gems/rake-13.2.1/lib/rake/application.rb:80:in `run'
/usr/local/lib/ruby/gems/3.2/gems/rake-13.2.1/exe/rake:27:in `<top (required)>'
/usr/local/bin/rake:25:in `load'
/usr/local/bin/rake:25:in `<top (required)>'
/usr/local/lib/ruby/gems/3.2/gems/bundler-2.5.14/lib/bundler/cli/exec.rb:58:in `load'
/usr/local/lib/ruby/gems/3.2/gems/bundler-2.5.14/lib/bundler/cli/exec.rb:58:in `kernel_load'
/usr/local/lib/ruby/gems/3.2/gems/bundler-2.5.14/lib/bundler/cli/exec.rb:23:in `run'
/usr/local/lib/ruby/gems/3.2/gems/bundler-2.5.14/lib/bundler/cli.rb:455:in `exec'
/usr/local/lib/ruby/gems/3.2/gems/bundler-2.5.14/lib/bundler/vendor/thor/lib/thor/command.rb:28:in `run'
/usr/local/lib/ruby/gems/3.2/gems/bundler-2.5.14/lib/bundler/vendor/thor/lib/thor/invocation.rb:127:in `invoke_command'
/usr/local/lib/ruby/gems/3.2/gems/bundler-2.5.14/lib/bundler/vendor/thor/lib/thor.rb:527:in `dispatch'
/usr/local/lib/ruby/gems/3.2/gems/bundler-2.5.14/lib/bundler/cli.rb:35:in `dispatch'
/usr/local/lib/ruby/gems/3.2/gems/bundler-2.5.14/lib/bundler/vendor/thor/lib/thor/base.rb:584:in `start'
/usr/local/lib/ruby/gems/3.2/gems/bundler-2.5.14/lib/bundler/cli.rb:29:in `start'
/usr/local/lib/ruby/gems/3.2/gems/bundler-2.5.14/exe/bundle:28:in `block in <top (required)>'
/usr/local/lib/ruby/gems/3.2/gems/bundler-2.5.14/lib/bundler/friendly_errors.rb:117:in `with_friendly_errors'
/usr/local/lib/ruby/gems/3.2/gems/bundler-2.5.14/exe/bundle:20:in `<top (required)>'
/usr/local/bin/bundle:25:in `load'
/usr/local/bin/bundle:25:in `<main>'
Tasks: TOP => db:migrate

Also, poking a bit more:

/usr/local/www/redmine # grep -r "stringify_keys" *
app/models/query.rb:      json[field] = options.stringify_keys
app/models/project.rb:    initialized = (attributes || {}).stringify_keys
app/models/issue.rb:    attrs.stringify_keys!
lib/plugins/acts_as_customizable/lib/acts_as_customizable.rb:            v = v.stringify_keys
lib/plugins/acts_as_customizable/lib/acts_as_customizable.rb:          values = values.stringify_keys
lib/plugins/acts_as_attachable/lib/acts_as_attachable.rb:            attachments = attachments.stringify_keys
lib/redmine/configuration.rb:        settings.stringify_keys!

oops, here:

gems/3.2/gems/activerecord-4.2.11.3/lib/active_record/connection_adapters/abstract_mysql_adapter.rb:        variables = @config.fetch(:variables, {}).stringify_keys

Cleaned up the gems files so the result is now:

# grep -r "variables, {}).stringify_keys" *
gems/3.2/gems/activerecord-6.1.7.8/lib/active_record/connection_adapters/postgresql_adapter.rb:          variables = @config.fetch(:variables, {}).stringify_keys
gems/3.2/gems/activerecord-6.1.7.8/lib/active_record/connection_adapters/abstract_mysql_adapter.rb:          variables = @config.fetch(:variables, {}).stringify_keys

Since mysql is configured it is almost certainly the second that is throwing the error.

Okay, the cause of the error is Rails which reads your config/database.yml. In your file, you have defined an empty variables section within your production environment, which is thus parsed as `nil`. To fix this, when not setting any variables, you should comment out (or remove) the variables section entirely from your database.yml, e.g.:

# Default setup is given for MySQL 5.7.7 or later.
# Examples for PostgreSQL, SQLite3 and SQL Server can be found at the end.
# Line indentation must be 2 spaces (no tabs).

production:
  adapter: mysql2
  database: redmine5t
  host: 10.3.69.183
  username: redmine5t
  password: "randompassword" 
  # Use "utf8" instead of "utfmb4" for MySQL prior to 5.7.7
  encoding: utf8mb4
  # variables:
  #   # Recommended `transaction_isolation` for MySQL to avoid concurrency issues is
  #   # `READ-COMMITTED`.
  #   # In case of MySQL lower than 8, the variable name is `tx_isolation`.
  #   # See https://www.redmine.org/projects/redmine/wiki/MySQL_configuration
  #   # should be updated to "transaction_isolation" after db update (then test)
  #   transaction_isolation: "tx_isolation" 

development:
  adapter: mysql2
  database: redmine_development
  host: localhost
  username: root
  password: "" 
  # Use "utf8" instead of "utfmb4" for MySQL prior to 5.7.7
  encoding: utf8mb4
  variables:
    transaction_isolation: "READ-COMMITTED" 

# Warning: The database defined as "test" will be erased and
# re-generated from your development database when you run "rake".
# Do not set this db to the same as development or production.
test:
  adapter: mysql2
  database: redmine_test
  host: localhost
  username: root
  password: "" 
  # Use "utf8" instead of "utfmb4" for MySQL prior to 5.7.7
  encoding: utf8mb4
  variables:
    transaction_isolation: "READ-COMMITTED" 

Figured it out - The problem is I commented out the recommended required value for transaction_isolation and you'll note my confused insertion of the key tx_isolation for the value in the pair.

Commenting out the key causes a null value to be passed to /abstract_mysql_adapter.rb:744 which doesn't have any input sanitizing. The undefined method error message is terribly misleading as the actual problem is a null value. My clue was this fine post: NoMethodError: undefined method for nil:NilClass... Explained

Armed with that data, I needed to decode why any of the possible values for transaction_isolation created a different error:

$ bundle config set --local without 'development test'
You are replacing the current local value of without, which is currently "development:test" 
$ RAILS_ENV=production bundle exec rake db:migrate --trace
(in /usr/local/www/redmine)
** Invoke db:migrate (first_time)
** Invoke db:load_config (first_time)
** Invoke environment (first_time)
** Execute environment
** Execute db:load_config
** Execute db:migrate
rake aborted!
ActiveRecord::StatementInvalid: Mysql2::Error: Unknown system variable 'transaction_isolation' (ActiveRecord::StatementInvalid)

It was not. Because above.

And it turns out that for MariaDB, at least MariaDB 10.5.16, the correct recommended required key value pair is:

And after that, it's just the usual quirks of Ruby. Now to flush and restart with the historical data.