Hi Jiri,
That functionality is not included in the DDT. What I am doing is creating a Post-Deploy Script with the TSQL code to add the indexes. To get the code right, I create the index in Management Studio, then generate a script and copy the data to the DDT script, here is a sample of my script:
/****** Object: Index [DuplicateImportCheck_idx] Script Date: 04/07/2010 09:50:41 ******/
IF EXISTS (SELECT * FROM sys.indexes WHERE object_id = OBJECT_ID(N'[dbo].[TransactionItemsImport]') AND name = N'DuplicateImportCheck_idx')
DROP INDEX [DuplicateImportCheck_idx] ON [dbo].[TransactionItemsImport] WITH ( ONLINE = OFF )
CREATE NONCLUSTERED INDEX [DuplicateImportCheck_idx] ON [dbo].[TransactionItemsImport]
(
[FK_Vendor_Carrier] ASC,
[FK_Transaction] ASC,
[ImportStatus] ASC
)
INCLUDE ( [FK_TransactionItems],
[FK_Items],
[CardLotNo],
[CardSerialNumber])
WITH (PAD_INDEX = OFF, STATISTICS_NORECOMPUTE = OFF, SORT_IN_TEMPDB = OFF, IGNORE_DUP_KEY = OFF, DROP_EXISTING = OFF, ONLINE = OFF, ALLOW_ROW_LOCKS = ON, ALLOW_PAGE_LOCKS = ON) ON [PRIMARY]
If I remember correctly there is an enhancement request for this feature, but don't know if the SF team will add it.