sql_io.py: put_table(): ignore(): Only delete from the insert_in_table, because the invalid rows only need to be removed from the rows that are actually being inserted into the DB. If there are invalid rows in the full (not uniquified) in_table, that's OK, as they can still get a valid output pkey if the first copy of a row they were considered a duplicate of is valid (this is a very unusual situation, so this change should not affect most real data).

sql_io.py: put_table(): ignore(): Merged filter_ var into sql.delete() call because that's the only place it's used

sql_io.py: put_table(): insert_into_pkeys(): Removed no longer used distinct param

sql_io.py: put_table(): Getting output table pkeys of existing/inserted rows: Don't DISTINCT ON the joined rows by input pkey, because this adds sorting overhead. This should not be needed because there generally should not be any duplicate rows for the columns in a unique index (if there are, this is an index configuration problem and should be fixed in the schema). It's possible that partial indexes (with a filter condition) were causing this, but testing without it in place will be needed to determine the cause.

sql.py: flatten(): Auto-add a pkey on the created temp table. This should be standard practice for most temp tables, and for sql_io.put_table() especially this will be useful if we ever want to add back sorting the in_table by row_num (possibly by CLUSTERing on the pkey to avoid pkey index scans).

sql.run_query_into() calls: Use new add_pkey_ param instead of manually calling sql.add_pkey()

sql.py: run_query_into(): Changed add_indexes_ param to add_pkey_ and add just a pkey if it's set. It's no longer necessary to create indexes on every column of a temp table, because the covering indexes for the join columns have been fixed to have columns in the same order as the output table's corresponding index so that they can be used for a merge join.

sql_io.py: put_table(): Add pkey on pkeys table right when it's created, so that any duplicates are detected right away instead of at the end of the iteration. (Duplicates are created as a result of joins matching multiple rows, which often indicates a database misconfiguration.)

sql_io.py: put_table(): Adding pkey on pkeys table: Removed log message because adding an index is considered a low-level operation, which isn't included in the Redmine SQL

schemas/tree_cross-links.sql: Ancestors table: Synced with current definition, which removes unneeded fki_* indexes. Note that the index on ancestor_id might be needed in the future if we ever want to get all the descendants of a plantname/namedplace or perform deletions on plantname/namedplace (which cascade to *_ancestor). For getting all the plantnames/namedplaces (of any rank) for a plantconcept/locationdetermination, though, the *_ancestor_pkey index is sufficient because plantname_id/namedplace_id is the first column in it.