I've been experimenting with tup and a recent change resulting in an error:

tup error: The database changed while refactoring. Tup should have caught 
this change before here and reported it as an error. Please run 'tup 
refactor --debug-sql' and send the output to the [email protected] 
mailing list.

So as requested here is the output
[0.000000s] {0} begin
[0.000000s] {0} select rval from config where lval=? ['db_version']
[0.000000s] {0} select rval from config where lval=? ['parser_version']
[0.000000s] {0} commit
[0.000000s] {0} begin
[0.000000s] {0} select rval from config where lval=? ['full_deps']
[0.000000s] {0} commit
[ tup ] [0.000s] Scanning filesystem...
[0.000000s] {0} begin
[0.000000s] {0} select id, dir, type, mtime, srcid, name from node where 
type=? or type=? or type=? or type=? [0, 2, 4]
[0.000000s] {0} select dir, type, mtime, srcid, name from node where id=? 
[22]
[0.001000s] {0} select dir, type, mtime, srcid, name from node where id=? 
[22]
[0.000000s] {0} insert or ignore into modify_list values(?) [21]
[0.001000s] {0} insert or ignore into create_list select to_id from 
normal_link, node where from_id=? and to_id=id and type=? [21, 2]
[0.000000s] {0} insert or ignore into config_list select to_id from 
normal_link, node where from_id=? and to_id=id and type=? [21, 0]
[0.000000s] {1} update node set mtime=? where id=? [1424390329, 21]
[0.004001s] {1} commit
[0.000000s] {1} begin
[0.000000s] {1} select * from config_list
[ tup ] [0.015s] Reading in new environment variables...
[0.000000s] {1} select dir, type, mtime, srcid, name from node where id=? 
[25]
[0.000000s] {1} select dir, type, mtime, srcid, name from node where id=? 
[26]
[0.000000s] {1} select dir, type, mtime, srcid, name from node where id=? 
[27]
[0.000000s] {1} select dir, type, mtime, srcid, name from node where id=? 
[28]
[0.000000s] {1} select dir, type, mtime, srcid, name from node where id=? 
[23]
[0.000000s] {1} select dir, type, mtime, srcid, name from node where id=? 
[24]
[0.000000s] {1} select dir, type, mtime, srcid, name from node where id=? 
[29]
[0.000000s] {1} select dir, type, mtime, srcid, name from node where id=? 
[30]
[0.000000s] {1} select dir, type, mtime, srcid, name from node where id=? 
[31]
[0.000000s] {1} select dir, type, mtime, srcid, name from node where id=? 
[32]
[0.000000s] {1} select dir, type, mtime, srcid, name from node where id=? 
[33]
[0.000000s] {1} select dir, type, mtime, srcid, name from node where id=? 
[34]
[0.000000s] {1} select dir, type, mtime, srcid, name from node where id=? 
[34]
[0.000000s] {1} commit
[0.000000s] {1} begin
[0.000000s] {1} select * from create_list
[0.000000s] {1} select to_id from normal_link where from_id=? [19]
[0.000000s] {1} select to_id from normal_link where from_id=? [16]
[0.000000s] {1} select to_id from normal_link where from_id=? [14]
[0.000000s] {1} select to_id from normal_link where from_id=? [10]
[0.000000s] {1} select to_id from normal_link where from_id=? [1]
[ tup ] [0.017s] Parsing Tupfiles...
[0.000000s] {1} select id from node where dir=? and type=? [1, 1]
[0.000000s] {1} select id from node where srcid=? and type=? [1, 4]
[0.000000s] {1} select id from node where dir=? and type=? [1, 1]
[0.001000s] {1} select id, type, mtime, srcid from node where dir=? and 
name=? collate nocase [1, 'Tuprules.tup']
[0.000000s] {1} select id, type, mtime, srcid from node where dir=? and 
name=? collate nocase [1, '.gitignore']
[0.000000s] {1} select id, type, mtime, srcid from node where dir=? and 
name=? collate nocase [1, 'Tupdefault.lua']
[0.000000s] {1} select id, type, mtime, srcid from node where dir=? and 
name=? collate nocase [1, 'Tupfile.lua']
[0.000000s] {1} select id, type, mtime, srcid from node where dir=? and 
name=? collate nocase [1, 'Tupfile']
[0.000000s] {1} select from_id from normal_link where to_id=? [1]
[0.000000s] {1} select from_id from sticky_link where to_id=? [1]
  20% 1) [0.002s] .
[0.000000s] {1} delete from create_list where id=? [1]
[0.001001s] {1} select id from node where dir=? and type=? [10, 1]
[0.000000s] {1} select id from node where srcid=? and type=? [10, 4]
[0.000000s] {1} select id from node where dir=? and type=? [10, 1]
[0.001000s] {1} select id, name, type, mtime, srcid from node where dir=? 
and (type=? or type=? or type=?) and name glob ? collate nocase [10, 0, 4, 
4, '*.c']
[0.000000s] {1} select id, type, mtime, srcid from node where dir=? and 
name=? collate nocase [1, 'objs']
[0.000000s] {1} update node set type=? where id=? [7, 266]
[0.000000s] {1} insert or ignore into modify_list values(?) [266]
[0.000000s] {1} select dir, type, mtime, srcid, name from node where id=? 
[398]
[0.000000s] {1} select dir, type, mtime, srcid, name from node where id=? 
[398]
[0.000000s] {1} select id, type, mtime, srcid from node where dir=? and 
name=? collate nocase [266, '<liba>']
[0.000000s] {1} select to_id from normal_link where from_id=? [398]
[0.000000s] {1} select from_id from sticky_link where to_id=? [398]
[0.000000s] {1} select id, type, mtime, srcid from node where dir=? and 
name=? collate nocase [1, 'libs']
[0.000000s] {1} update node set type=? where id=? [7, 270]
[0.000000s] {1} insert or ignore into modify_list values(?) [270]
[0.000000s] {1} select dir, type, mtime, srcid, name from node where id=? 
[399]
[0.000000s] {1} select dir, type, mtime, srcid, name from node where id=? 
[399]
[0.000000s] {1} select id, type, mtime, srcid from node where dir=? and 
name=? collate nocase [270, '<libraries>']
[0.000000s] {1} select to_id from normal_link where from_id=? [399]
[0.000000s] {1} select from_id from sticky_link where to_id=? [399]
[0.000000s] {1} select id, type, mtime, srcid from node where dir=? and 
name=? collate nocase [10, '.gitignore']
[0.000000s] {1} select id, type, mtime, srcid from node where dir=? and 
name=? collate nocase [10, 'Tuprules.lua']
[0.000000s] {1} select id, type, mtime, srcid from node where dir=? and 
name=? collate nocase [9, 'Tuprules.lua']
[0.000000s] {1} select id, type, mtime, srcid from node where dir=? and 
name=? collate nocase [10, 'Tupfile']
[0.000000s] {1} select from_id from normal_link where to_id=? [10]
[0.000000s] {1} select from_id from sticky_link where to_id=? [10]
  40% 2) [0.035s] src\lib_a
[0.000000s] {1} delete from create_list where id=? [10]
[0.000000s] {1} select id from node where dir=? and type=? [14, 1]
[0.000000s] {1} select id from node where srcid=? and type=? [14, 4]
[0.000000s] {1} select id from node where dir=? and type=? [14, 1]
[0.001000s] {1} select id, name, type, mtime, srcid from node where dir=? 
and (type=? or type=? or type=?) and name glob ? collate nocase [14, 0, 4, 
4, '*.c']
[0.000000s] {1} select dir, type, mtime, srcid, name from node where id=? 
[392]
[0.000000s] {1} select dir, type, mtime, srcid, name from node where id=? 
[392]
[0.000000s] {1} select to_id from normal_link where from_id=? [392]
[0.000000s] {1} select from_id from sticky_link where to_id=? [392]
[0.000000s] {1} select id, type, mtime, srcid from node where dir=? and 
name=? collate nocase [14, '.gitignore']
[0.000000s] {1} select id, type, mtime, srcid from node where dir=? and 
name=? collate nocase [14, 'Tuprules.lua']
[0.000000s] {1} select id, type, mtime, srcid from node where dir=? and 
name=? collate nocase [13, 'Tuprules.lua']
[0.000000s] {1} select id, type, mtime, srcid from node where dir=? and 
name=? collate nocase [14, 'Tupfile']
[0.000000s] {1} select from_id from normal_link where to_id=? [14]
[0.000000s] {1} select from_id from sticky_link where to_id=? [14]
  60% 3) [0.005s] src\lib_a\os\win32
[0.000000s] {1} delete from create_list where id=? [14]
[0.000000s] {1} select id from node where dir=? and type=? [16, 1]
[0.000000s] {1} select id from node where srcid=? and type=? [16, 4]
[0.000000s] {1} select id from node where dir=? and type=? [16, 1]
[0.000000s] {1} select id, name, type, mtime, srcid from node where dir=? 
and (type=? or type=? or type=?) and name glob ? collate nocase [16, 0, 4, 
4, '*.c']
[0.000000s] {1} select dir, type, mtime, srcid, name from node where id=? 
[409]
[0.000000s] {1} select dir, type, mtime, srcid, name from node where id=? 
[409]
[0.000000s] {1} select id, type, mtime, srcid from node where dir=? and 
name=? collate nocase [266, '<objects>']
[0.000000s] {1} select to_id from normal_link where from_id=? [409]
[0.000000s] {1} select from_id from sticky_link where to_id=? [409]
[0.000000s] {1} select dir, type, mtime, srcid, name from node where id=? 
[416]
[0.000000s] {1} select dir, type, mtime, srcid, name from node where id=? 
[416]
[0.000000s] {1} select to_id from normal_link where from_id=? [416]
[0.000000s] {1} select from_id from sticky_link where to_id=? [416]
[0.000000s] {1} select id, type, mtime, srcid from node where dir=? and 
name=? collate nocase [16, '.gitignore']
[0.000000s] {1} select id, type, mtime, srcid from node where dir=? and 
name=? collate nocase [16, 'Tuprules.lua']
[0.000000s] {1} select id, type, mtime, srcid from node where dir=? and 
name=? collate nocase [16, 'Tupfile']
[0.000000s] {1} select from_id from normal_link where to_id=? [16]
[0.000000s] {1} select from_id from sticky_link where to_id=? [16]
  80% 4) [0.117s] src\lib_a\test
[0.000000s] {1} delete from create_list where id=? [16]
[0.000000s] {1} select id from node where dir=? and type=? [19, 1]
[0.000000s] {1} select id from node where srcid=? and type=? [19, 4]
[0.000000s] {1} select id from node where dir=? and type=? [19, 1]
[0.000000s] {1} select id, name, type, mtime, srcid from node where dir=? 
and (type=? or type=? or type=?) and name glob ? collate nocase [19, 0, 4, 
4, '*.cpp']
[0.000000s] {1} select dir, type, mtime, srcid, name from node where id=? 
[422]
[0.000000s] {1} select dir, type, mtime, srcid, name from node where id=? 
[422]
[0.000000s] {1} select id, type, mtime, srcid from node where dir=? and 
name=? collate nocase [266, '<libb>']
[0.000000s] {1} select to_id from normal_link where from_id=? [422]
[0.000000s] {1} select from_id from sticky_link where to_id=? [422]
[0.000000s] {1} select dir, type, mtime, srcid, name from node where id=? 
[424]
[0.000000s] {1} select dir, type, mtime, srcid, name from node where id=? 
[424]
[0.000000s] {1} select to_id from normal_link where from_id=? [424]
[0.000000s] {1} select from_id from sticky_link where to_id=? [424]
[0.000000s] {1} select id, type, mtime, srcid from node where dir=? and 
name=? collate nocase [19, '.gitignore']
[0.000000s] {1} select id, type, mtime, srcid from node where dir=? and 
name=? collate nocase [19, 'Tuprules.lua']
[0.000000s] {1} select id, type, mtime, srcid from node where dir=? and 
name=? collate nocase [19, 'Tupfile']
[0.000000s] {1} select from_id from normal_link where to_id=? [19]
[0.000000s] {1} select from_id from sticky_link where to_id=? [19]
 100% 5) [0.004s] src\lib_b
[0.000000s] {1} delete from create_list where id=? [19]
[ tup ] [0.184s] No files to delete.
[0.000000s] {1} select exists(select 1 from node where dir=? and (type=? or 
type=?)) [1, 0, 2]
[0.000000s] {1} select exists(select 1 from node where dir=? and (type=? or 
type=?)) [10, 0, 2]
[0.000000s] {1} select exists(select 1 from node where dir=? and (type=? or 
type=?)) [14, 0, 2]
[0.000000s] {1} select exists(select 1 from node where dir=? and (type=? or 
type=?)) [16, 0, 2]
[0.000000s] {1} select exists(select 1 from node where dir=? and (type=? or 
type=?)) [19, 0, 2]
tup error: The database changed while refactoring. Tup should have caught 
this change before here and reported it as an error. Please run 'tup 
refactor --debug-sql' and send the output to the [email protected] 
mailing list.
[0.001001s] {1} rollback

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