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The Query Options found under the [Query Menu] allows enabling/disabling [Quote Identifiers], [Auto Join on Foreign Key], [Schema Qualified Tables], [Database Qualified Tables] and [Ignore Unused Tables in Diagram]. The contents of the [Query Menu] choices varies based on the database vendor and version connected to. The Query Options control how the SQL in the SQL Pane is written.
The Query Options are extremely important when attempting to create cross database or cross schema queries. It's a good idea to enable both [Schema Qualified Tables] and [Database Qualified Tables] if you know you will be creating Cross Database, Multi-Database or Cross Schema queries. Enabling them allows the Query Builder to distinguish between tables with the same name that reside on different databases or schemas. See Multi-Database Query page for more details.
When [Ignore Unused Tables in Diagram] is enabled this prevents any of the tables in the diagram which have not had an item dragged into a deck from being appearing in the SQL of the SQL Pane. Orange header text and orange join lines indicate the presence of unused tables.
If you create a join between two or more tables, and any of those tables is considered unused (orange), then none of the tables in the join will appear in the SQL. Enabling the [Ignore Unused Tables in Diagram] option is useful if there are many Table Entities in the Entity Pane, but you only want to execute on those which have items dragged into one of the decks.
[Auto Join on Foreign Key] does not affect preexisting entities in the Diagram Pane. It will only take affect on items placed after it has been enabled.