Here are some considerations for SQL File format and deployment.

You will need to end file / if it contains Package Specification, Package Body, Trigger.

CREATE OR REPLACE PACKAGE xxhr_bipub_rep_pkg AS

   PROCEDURE generate_xml(p_errbuf  OUT VARCHAR2
                         ,p_retcode OUT NUMBER);

END xxhr_bipub_rep_pkg;
/

Consider adding compileInvalidSqls operation in Deploy workflow if SQL files are being deployed. This operation can take longer if there are many invalid objects in Schema.
Custom objects in non APPS schema with grants to APPS user. It is recommended by Oracle to create custom objects in custom schema. You need to provide Grants to APPS user to these custom objects. You can achieve this in two different ways in FlexDeploy.
1. Give necessary rights to APPS user, so it can select on any other schema objects. For example, SELECT ANY TABLE privilege can be given to APPS and similarly other ANY type Grants can be given to APPS user.
2. Use custom schema user in FlexDeploy to create objects and grant to APPS.
  1. Create custom user and password properties on Deploy workflow to be at Environment Instance Scope. For example,
  2. Defined values for these user and password in various Environment Instance pages in Topology.
  3. Use custom properties on Project Files tab for specific Files.