I also posted this to stackoverflow since I wasn't sure which way of asking 
questions like this is preferred.
http://stackoverflow.com/questions/17024482/h2-database-unsuccessful-schema-statement-when-add-index-and-foreign-key-constra

H2 does not appear to support the index/FK syntax generated by hibernate 
for the MySQL5 dialects when using ;MODE=MYSQL and hibernate with a dialect 
of org.hibernate.dialect.MySQL5Dialect.

My goal here is to have one set of SQL scripts and use hibernate for the 
ORM parts. Everything works fine in MySQL 5.5 but when I try to use H2 for 
things like unit tests and starting up a demo version of my app I get 
hundreds of failures from hibernate generated alter table statements as 
shown below. Unfortunately, I have not been able to find a way to get 
hibernate to change the way the statements are generated but that might be 
an option as well. I tried using org.hibernate.dialect.H2Dialect but that 
produces more severe errors so I don't think that will work.

alter table SAM_PUBLISHEDSECUREDIP_T
  add index FK1EDEA25B9482C945 (ASSESSMENTID), 
  add constraint FK1EDEA25B9482C945 foreign key (ASSESSMENTID) 
  references SAM_PUBLISHEDASSESSMENT_T (ID)

Results in an error like this in H2:

org.h2.jdbc.JdbcSQLException: Syntax error in SQL statement "ALTER TABLE 
SAM_PUBLISHEDSECUREDIP_T ADD INDEX FK1EDEA25B9482C945 (ASSESSMENTID),[*] 
ADD CONSTRAINT FK1EDEA25B9482C945 FOREIGN KEY (ASSESSMENTID) REFERENCES 
SAM_PUBLISHEDASSESSMENT_T (ID) "; SQL statement: alter table 
SAM_PUBLISHEDSECUREDIP_T add index FK1EDEA25B9482C945 (ASSESSMENTID), add 
constraint FK1EDEA25B9482C945 foreign key (ASSESSMENTID) references 
SAM_PUBLISHEDASSESSMENT_T (ID) [42000-172]

NOTE: I am open to writing and providing a patch for H2 but I could use 
some tips on where to look in that codebase.

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