Is there anyway to make sql server search the master database for SQLCLR stored procedures before the current one?
I don't know a solution (and I don't know if the CLR scaffolding was ever designed to mimic the functionality you're talking about), but one workaround could be to create a T-SQL stored procedure in master that serves as a wrapper to relay the call to the CLR version. Marking it as a system object shouldn't be necessary, as long as a stored procedure with the same name doesn't exist in the user database.

EDIT - just proved that this works fine, as much for myself as anything. First I created your assembly and added the procedure necessary to repro (I'm not going to include all the bits here for brevity):

USE master;
GO
CREATE ASSEMBLY [Justin]
    AUTHORIZATION [dbo]
    FROM 0x4D5A900003000000040... lots of data here ...;
GO
ALTER ASSEMBLY [Justin]
    DROP FILE ALL
    ADD FILE FROM 0x4D6963726F... even more data here ...;
    AS N'Justin.pdb';
GO
CREATE PROCEDURE [dbo].[sp_RAISERROR_CaughtDemo]
AS EXTERNAL NAME [Justin].[StoredProcedures].[RaiserrorCaught]
GO


Then I created a wrapper stored procedure, making sure to fully qualify the CLR procedure:

CREATE PROCEDURE dbo.sp_RAISERROR_CaughtDemo_Wrapper
AS
BEGIN
    SET NOCOUNT ON;
    EXEC master.dbo.sp_RAISERROR_CaughtDemo;
END
GO


Then I adjusted your repro code to call the wrapper from tempdb instead:

USE tempdb;
PRINT 'USING tempDb';
EXEC sp_RAISERROR_CaughtDemo_wrapper;
GO


Results:

USING tempDb
RAISERROR() Caught Severity 0
RAISERROR() Caught Severity 1
Msg 50000, Level 1, State 1
RAISERROR() Caught Severity 2
Msg 50000, Level 2, State 1
RAISERROR() Caught Severity 3
Msg 50000, Level 3, State 1
RAISERROR() Caught Severity 4
Msg 50000, Level 4, State 1
RAISERROR() Caught Severity 5
Msg 50000, Level 5, State 1
RAISERROR() Caught Severity 6
Msg 50000, Level 6, State 1
RAISERROR() Caught Severity 7
Msg 50000, Level 7, State 1
RAISERROR() Caught Severity 8
Msg 50000, Level 8, State 1
RAISERROR() Caught Severity 9
Msg 50000, Level 9, State 1
RAISERROR() Caught Severity 10
Msg 50000, Level 11, State 1, Line 1
RAISERROR() Caught Severity 11


So this shows that you should be able to use a wrapper like this to be able to call CLR procedures, unreferenced, from other databases.

(However, I will suggest that in general this shouldn't be a goal - you should be properly defining references with three-part names where applicable.)

I'll confess I did make one change to your stored procedure though, to prevent Visual Studio from whining at me. I changed:

while (true)


To:

while (i &lt;= 11)


But of course this change had nothing to do with the scoping issue.