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+### Please describe the problem.
+
+On two hosts, I've configured two separate local repositories (~/foo and ~/bar) with the assistant and added a transfer repository to ~/foo.
+
+While files are kept separate, the configuration seems to get mixed up. This results in all files beeing uploaded to the configured transfer repository.
+
+The reason might be, that informations about ~/bar are included in the configuration of ~/foo (see below).
+
+### What steps will reproduce the problem?
+
+* Create local repository ~/foo on both hosts
+* Add transfer repository to ~/foo on both hosts
+* Add some files to ~/foo and let it sync
+* Create local repository ~/bar and select keep the repositories separate on both hosts
+* All files of ~/foo will now be uploaded again to the transfer repository
+
+### What version of git-annex are you using? On what operating system?
+
+5.20140421~bpo70+1 on Debian 7.5 amd64
+
+### Please provide any additional information below.
+
+*trh@czc4142wfz:~/foo$ git-annex info*
+<pre><code>repository mode: direct
+trusted repositories: 0
+semitrusted repositories: 4
+	00000000-0000-0000-0000-000000000001 -- web
+ 	bd23a5ed-af6e-466d-ac8c-9ea38a220c62 -- trh@r9-y3pll:~/foo
+ 	cc888105-b6c3-4926-8396-e3870f6bfc05 -- transfer_foo
+ 	f3b332fd-4b7a-4a5b-b077-8f13d3d9a407 -- here (trh@czc4142wfz:~/foo)
+untrusted repositories: 0
+transfers in progress: none
+available local disk space: 356.11 gigabytes (+1 megabyte reserved)
+local annex keys: 2
+local annex size: 2.99 gigabytes
+annexed files in working tree: 2
+size of annexed files in working tree: 2.99 gigabytes
+bloom filter size: 16 mebibytes (0% full)
+backend usage: 
+	SHA256E: 4
+</code></pre>
+
+*trh@czc4142wfz:~/bar$ git-annex info*
+<pre><code>repository mode: direct
+trusted repositories: 0
+semitrusted repositories: 2
+	00000000-0000-0000-0000-000000000001 -- web
+ 	f1478436-cf7b-4a05-91a6-91157ae5e9c4 -- here (trh@czc4142wfz:~/bar)
+untrusted repositories: 0
+transfers in progress: none
+available local disk space: 356.11 gigabytes (+1 megabyte reserved)
+local annex keys: 0
+local annex size: 0 bytes
+annexed files in working tree: 0
+size of annexed files in working tree: 0 bytes
+bloom filter size: 16 mebibytes (0% full)
+backend usage: 
+</code></pre>
+
+*trh@czc4142wfz:~/foo$ git-annex vicfg*
+<pre><code># git-annex configuration
+#
+# Changes saved to this file will be recorded in the git-annex branch.
+#
+# Lines in this file have the format:
+#   setting field = value
+
+# Repository trust configuration
+# (Valid trust levels: trusted semitrusted untrusted dead)
+# (for web)
+#trust 00000000-0000-0000-0000-000000000001 = semitrusted
+# (for trh@r9-y3pll:~/foo)
+#trust bd23a5ed-af6e-466d-ac8c-9ea38a220c62 = semitrusted
+# (for transfer_foo)
+#trust cc888105-b6c3-4926-8396-e3870f6bfc05 = semitrusted
+# (for trh@czc4142wfz:~/foo)
+#trust f3b332fd-4b7a-4a5b-b077-8f13d3d9a407 = semitrusted
+
+# Repository groups
+# (Standard groups: client transfer backup incrementalbackup smallarchive archive source manual public unwanted)
+# (Separate group names with spaces)
+# (for )
+group 357eaef4-af1b-491a-a003-01c2d583056e = client
+# (for trh@r9-y3pll:~/foo)
+group bd23a5ed-af6e-466d-ac8c-9ea38a220c62 = client
+# (for )
+group f1478436-cf7b-4a05-91a6-91157ae5e9c4 = client
+# (for trh@czc4142wfz:~/foo)
+group f3b332fd-4b7a-4a5b-b077-8f13d3d9a407 = client
+# (for transfer_foo)
+group cc888105-b6c3-4926-8396-e3870f6bfc05 = transfer
+# (for web)
+#group 00000000-0000-0000-0000-000000000001 =
+
+# Repository preferred contents
+# (for )
+wanted 357eaef4-af1b-491a-a003-01c2d583056e = standard
+# (for trh@r9-y3pll:~/foo)
+wanted bd23a5ed-af6e-466d-ac8c-9ea38a220c62 = standard
+# (for transfer_foo)
+wanted cc888105-b6c3-4926-8396-e3870f6bfc05 = standard
+# (for )
+wanted f1478436-cf7b-4a05-91a6-91157ae5e9c4 = standard
+# (for trh@czc4142wfz:~/foo)
+wanted f3b332fd-4b7a-4a5b-b077-8f13d3d9a407 = standard
+# (for web)
+#wanted 00000000-0000-0000-0000-000000000001 = standard
+
+# Group preferred contents
+# (Used by repositories with "groupwanted" in their preferred contents)
+#groupwanted archive = standard
+#groupwanted backup = standard
+#groupwanted client = standard
+#groupwanted incrementalbackup = standard
+#groupwanted manual = standard
+#groupwanted public = standard
+#groupwanted smallarchive = standard
+#groupwanted source = standard
+#groupwanted transfer = standard
+#groupwanted unwanted = standard
+
+# Standard preferred contents
+# (Used by wanted or groupwanted expressions containing "standard")
+# (For reference only; built-in and cannot be changed!)
+# standard client = (((exclude=*/archive/* and exclude=archive/*) or (not (copies=archive:1 or copies=smallarchive:1))) and not unused) or approxlackingcopies=1
+# standard transfer = (not (inallgroup=client and copies=client:2) and ((((exclude=*/archive/* and exclude=archive/*) or (not (copies=archive:1 or copies=smallarchive:1))) and not unused) or approxlackingcopies=1)) or approxlackingcopies=1
+# standard backup = include=* or unused
+# standard incrementalbackup = ((include=* or unused) and (not copies=incrementalbackup:1)) or approxlackingcopies=1
+# standard smallarchive = ((include=*/archive/* or include=archive/*) and ((not (copies=archive:1 or copies=smallarchive:1)) or approxlackingcopies=1)) or approxlackingcopies=1
+# standard archive = (not (copies=archive:1 or copies=smallarchive:1)) or approxlackingcopies=1
+# standard source = not (copies=1)
+# standard manual = present and ((((exclude=*/archive/* and exclude=archive/*) or (not (copies=archive:1 or copies=smallarchive:1))) and not unused) or approxlackingcopies=1)
+# standard public = inpreferreddir
+# standard unwanted = exclude=*
+
+# Repository required contents
+# (for web)
+#required 00000000-0000-0000-0000-000000000001 =
+# (for trh@r9-y3pll:~/foo)
+#required bd23a5ed-af6e-466d-ac8c-9ea38a220c62 =
+# (for transfer_foo)
+#required cc888105-b6c3-4926-8396-e3870f6bfc05 =
+# (for trh@czc4142wfz:~/foo)
+#required f3b332fd-4b7a-4a5b-b077-8f13d3d9a407 =
+
+# Scheduled activities
+# (Separate multiple activities with "; ")
+# (for web)
+#schedule 00000000-0000-0000-0000-000000000001 =
+# (for trh@r9-y3pll:~/foo)
+#schedule bd23a5ed-af6e-466d-ac8c-9ea38a220c62 =
+# (for transfer_foo)
+#schedule cc888105-b6c3-4926-8396-e3870f6bfc05 =
+# (for trh@czc4142wfz:~/foo)
+#schedule f3b332fd-4b7a-4a5b-b077-8f13d3d9a407 =
+</code></pre>
+
+**Note: f1478436-cf7b-4a05-91a6-91157ae5e9c4 is id of ~/bar on local host (see below) / 357eaef4-af1b-491a-a003-01c2d583056e is id of ~/bar on r9-y3pll**
+
+*trh@czc4142wfz:~/bar$ git-annex vicfg*
+<pre><code># git-annex configuration
+#
+# Changes saved to this file will be recorded in the git-annex branch.
+#
+# Lines in this file have the format:
+#   setting field = value
+
+# Repository trust configuration
+# (Valid trust levels: trusted semitrusted untrusted dead)
+# (for web)
+#trust 00000000-0000-0000-0000-000000000001 = semitrusted
+# (for trh@czc4142wfz:~/bar)
+#trust f1478436-cf7b-4a05-91a6-91157ae5e9c4 = semitrusted
+
+# Repository groups
+# (Standard groups: client transfer backup incrementalbackup smallarchive archive source manual public unwanted)
+# (Separate group names with spaces)
+# (for web)
+#group 00000000-0000-0000-0000-000000000001 =
+# (for trh@czc4142wfz:~/bar)
+#group f1478436-cf7b-4a05-91a6-91157ae5e9c4 =
+
+# Repository preferred contents
+# (for web)
+#wanted 00000000-0000-0000-0000-000000000001 = standard
+# (for trh@czc4142wfz:~/bar)
+#wanted f1478436-cf7b-4a05-91a6-91157ae5e9c4 = standard
+
+# Group preferred contents
+# (Used by repositories with "groupwanted" in their preferred contents)
+#groupwanted archive = standard
+#groupwanted backup = standard
+#groupwanted client = standard
+#groupwanted incrementalbackup = standard
+#groupwanted manual = standard
+#groupwanted public = standard
+#groupwanted smallarchive = standard
+#groupwanted source = standard
+#groupwanted transfer = standard
+#groupwanted unwanted = standard
+
+# Standard preferred contents
+# (Used by wanted or groupwanted expressions containing "standard")
+# (For reference only; built-in and cannot be changed!)
+# standard client = (((exclude=*/archive/* and exclude=archive/*) or (not (copies=archive:1 or copies=smallarchive:1))) and not unused) or approxlackingcopies=1
+# standard transfer = (not (inallgroup=client and copies=client:2) and ((((exclude=*/archive/* and exclude=archive/*) or (not (copies=archive:1 or copies=smallarchive:1))) and not unused) or approxlackingcopies=1)) or approxlackingcopies=1
+# standard backup = include=* or unused
+# standard incrementalbackup = ((include=* or unused) and (not copies=incrementalbackup:1)) or approxlackingcopies=1
+# standard smallarchive = ((include=*/archive/* or include=archive/*) and ((not (copies=archive:1 or copies=smallarchive:1)) or approxlackingcopies=1)) or approxlackingcopies=1
+# standard archive = (not (copies=archive:1 or copies=smallarchive:1)) or approxlackingcopies=1
+# standard source = not (copies=1)
+# standard manual = present and ((((exclude=*/archive/* and exclude=archive/*) or (not (copies=archive:1 or copies=smallarchive:1))) and not unused) or approxlackingcopies=1)
+# standard public = inpreferreddir
+# standard unwanted = exclude=*
+
+# Repository required contents
+# (for web)
+#required 00000000-0000-0000-0000-000000000001 =
+# (for trh@czc4142wfz:~/bar)
+#required f1478436-cf7b-4a05-91a6-91157ae5e9c4 =
+
+# Scheduled activities
+# (Separate multiple activities with "; ")
+# (for web)
+#schedule 00000000-0000-0000-0000-000000000001 =
+# (for trh@czc4142wfz:~/bar)
+#schedule f1478436-cf7b-4a05-91a6-91157ae5e9c4 =
+</code></pre>
+
+*trh@r9-y3pll:~/foo$ git-annex info*
+<pre><code>repository mode: direct
+trusted repositories: 0
+semitrusted repositories: 4
+	00000000-0000-0000-0000-000000000001 -- web
+ 	bd23a5ed-af6e-466d-ac8c-9ea38a220c62 -- here (trh@r9-y3pll:~/foo)
+ 	cc888105-b6c3-4926-8396-e3870f6bfc05 -- transfer_foo
+ 	f3b332fd-4b7a-4a5b-b077-8f13d3d9a407 -- trh@czc4142wfz:~/foo
+untrusted repositories: 0
+transfers in progress: none
+available local disk space: 280.24 gigabytes (+1 megabyte reserved)
+local annex keys: 2
+local annex size: 2.99 gigabytes
+annexed files in working tree: 2
+size of annexed files in working tree: 2.99 gigabytes
+bloom filter size: 16 mebibytes (0% full)
+backend usage: 
+	SHA256E: 4
+</code></pre>
+
+*trh@r9-y3pll:~/bar$ git-annex info*
+<pre><code>repository mode: direct
+trusted repositories: 0
+semitrusted repositories: 2
+	00000000-0000-0000-0000-000000000001 -- web
+ 	357eaef4-af1b-491a-a003-01c2d583056e -- here (trh@r9-y3pll:~/bar)
+untrusted repositories: 0
+transfers in progress: none
+available local disk space: 280.24 gigabytes (+1 megabyte reserved)
+local annex keys: 0
+local annex size: 0 bytes
+annexed files in working tree: 0
+size of annexed files in working tree: 0 bytes
+bloom filter size: 16 mebibytes (0% full)
+backend usage: 
+</code></pre>
+
+*trh@r9-y3pll:~/foo$ git-annex vicfg*
+<pre><code># git-annex configuration
+#
+# Changes saved to this file will be recorded in the git-annex branch.
+#
+# Lines in this file have the format:
+#   setting field = value
+
+# Repository trust configuration
+# (Valid trust levels: trusted semitrusted untrusted dead)
+# (for web)
+#trust 00000000-0000-0000-0000-000000000001 = semitrusted
+# (for trh@r9-y3pll:~/foo)
+#trust bd23a5ed-af6e-466d-ac8c-9ea38a220c62 = semitrusted
+# (for transfer_foo)
+#trust cc888105-b6c3-4926-8396-e3870f6bfc05 = semitrusted
+# (for trh@czc4142wfz:~/foo)
+#trust f3b332fd-4b7a-4a5b-b077-8f13d3d9a407 = semitrusted
+
+# Repository groups
+# (Standard groups: client transfer backup incrementalbackup smallarchive archive source manual public unwanted)
+# (Separate group names with spaces)
+# (for )
+group 357eaef4-af1b-491a-a003-01c2d583056e = client
+# (for trh@r9-y3pll:~/foo)
+group bd23a5ed-af6e-466d-ac8c-9ea38a220c62 = client
+# (for )
+group f1478436-cf7b-4a05-91a6-91157ae5e9c4 = client
+# (for trh@czc4142wfz:~/foo)
+group f3b332fd-4b7a-4a5b-b077-8f13d3d9a407 = client
+# (for transfer_foo)
+group cc888105-b6c3-4926-8396-e3870f6bfc05 = transfer
+# (for web)
+#group 00000000-0000-0000-0000-000000000001 =
+
+# Repository preferred contents
+# (for )
+wanted 357eaef4-af1b-491a-a003-01c2d583056e = standard
+# (for trh@r9-y3pll:~/foo)
+wanted bd23a5ed-af6e-466d-ac8c-9ea38a220c62 = standard
+# (for transfer_foo)
+wanted cc888105-b6c3-4926-8396-e3870f6bfc05 = standard
+# (for )
+wanted f1478436-cf7b-4a05-91a6-91157ae5e9c4 = standard
+# (for trh@czc4142wfz:~/foo)
+wanted f3b332fd-4b7a-4a5b-b077-8f13d3d9a407 = standard
+# (for web)
+#wanted 00000000-0000-0000-0000-000000000001 = standard
+
+# Group preferred contents
+# (Used by repositories with "groupwanted" in their preferred contents)
+#groupwanted archive = standard
+#groupwanted backup = standard
+#groupwanted client = standard
+#groupwanted incrementalbackup = standard
+#groupwanted manual = standard
+#groupwanted public = standard
+#groupwanted smallarchive = standard
+#groupwanted source = standard
+#groupwanted transfer = standard
+#groupwanted unwanted = standard
+
+# Standard preferred contents
+# (Used by wanted or groupwanted expressions containing "standard")
+# (For reference only; built-in and cannot be changed!)
+# standard client = (((exclude=*/archive/* and exclude=archive/*) or (not (copies=archive:1 or copies=smallarchive:1))) and not unused) or approxlackingcopies=1
+# standard transfer = (not (inallgroup=client and copies=client:2) and ((((exclude=*/archive/* and exclude=archive/*) or (not (copies=archive:1 or copies=smallarchive:1))) and not unused) or approxlackingcopies=1)) or approxlackingcopies=1
+# standard backup = include=* or unused
+# standard incrementalbackup = ((include=* or unused) and (not copies=incrementalbackup:1)) or approxlackingcopies=1
+# standard smallarchive = ((include=*/archive/* or include=archive/*) and ((not (copies=archive:1 or copies=smallarchive:1)) or approxlackingcopies=1)) or approxlackingcopies=1
+# standard archive = (not (copies=archive:1 or copies=smallarchive:1)) or approxlackingcopies=1
+# standard source = not (copies=1)
+# standard manual = present and ((((exclude=*/archive/* and exclude=archive/*) or (not (copies=archive:1 or copies=smallarchive:1))) and not unused) or approxlackingcopies=1)
+# standard public = inpreferreddir
+# standard unwanted = exclude=*
+
+# Repository required contents
+# (for web)
+#required 00000000-0000-0000-0000-000000000001 =
+# (for trh@r9-y3pll:~/foo)
+#required bd23a5ed-af6e-466d-ac8c-9ea38a220c62 =
+# (for transfer_foo)
+#required cc888105-b6c3-4926-8396-e3870f6bfc05 =
+# (for trh@czc4142wfz:~/foo)
+#required f3b332fd-4b7a-4a5b-b077-8f13d3d9a407 =
+
+# Scheduled activities
+# (Separate multiple activities with "; ")
+# (for web)
+#schedule 00000000-0000-0000-0000-000000000001 =
+# (for trh@r9-y3pll:~/foo)
+#schedule bd23a5ed-af6e-466d-ac8c-9ea38a220c62 =
+# (for transfer_foo)
+#schedule cc888105-b6c3-4926-8396-e3870f6bfc05 =
+# (for trh@czc4142wfz:~/foo)
+#schedule f3b332fd-4b7a-4a5b-b077-8f13d3d9a407 =
+</code></pre>
+
+*trh@r9-y3pll:~/bar$ git-annex vicfg*
+<pre><code># git-annex configuration
+#
+# Changes saved to this file will be recorded in the git-annex branch.
+#
+# Lines in this file have the format:
+#   setting field = value
+
+# Repository trust configuration
+# (Valid trust levels: trusted semitrusted untrusted dead)
+# (for web)
+#trust 00000000-0000-0000-0000-000000000001 = semitrusted
+# (for trh@r9-y3pll:~/bar)
+#trust 357eaef4-af1b-491a-a003-01c2d583056e = semitrusted
+
+# Repository groups
+# (Standard groups: client transfer backup incrementalbackup smallarchive archive source manual public unwanted)
+# (Separate group names with spaces)
+# (for web)
+#group 00000000-0000-0000-0000-000000000001 =
+# (for trh@r9-y3pll:~/bar)
+#group 357eaef4-af1b-491a-a003-01c2d583056e =
+
+# Repository preferred contents
+# (for web)
+#wanted 00000000-0000-0000-0000-000000000001 = standard
+# (for trh@r9-y3pll:~/bar)
+#wanted 357eaef4-af1b-491a-a003-01c2d583056e = standard
+
+# Group preferred contents
+# (Used by repositories with "groupwanted" in their preferred contents)
+#groupwanted archive = standard
+#groupwanted backup = standard
+#groupwanted client = standard
+#groupwanted incrementalbackup = standard
+#groupwanted manual = standard
+#groupwanted public = standard
+#groupwanted smallarchive = standard
+#groupwanted source = standard
+#groupwanted transfer = standard
+#groupwanted unwanted = standard
+
+# Standard preferred contents
+# (Used by wanted or groupwanted expressions containing "standard")
+# (For reference only; built-in and cannot be changed!)
+# standard client = (((exclude=*/archive/* and exclude=archive/*) or (not (copies=archive:1 or copies=smallarchive:1))) and not unused) or approxlackingcopies=1
+# standard transfer = (not (inallgroup=client and copies=client:2) and ((((exclude=*/archive/* and exclude=archive/*) or (not (copies=archive:1 or copies=smallarchive:1))) and not unused) or approxlackingcopies=1)) or approxlackingcopies=1
+# standard backup = include=* or unused
+# standard incrementalbackup = ((include=* or unused) and (not copies=incrementalbackup:1)) or approxlackingcopies=1
+# standard smallarchive = ((include=*/archive/* or include=archive/*) and ((not (copies=archive:1 or copies=smallarchive:1)) or approxlackingcopies=1)) or approxlackingcopies=1
+# standard archive = (not (copies=archive:1 or copies=smallarchive:1)) or approxlackingcopies=1
+# standard source = not (copies=1)
+# standard manual = present and ((((exclude=*/archive/* and exclude=archive/*) or (not (copies=archive:1 or copies=smallarchive:1))) and not unused) or approxlackingcopies=1)
+# standard public = inpreferreddir
+# standard unwanted = exclude=*
+
+# Repository required contents
+# (for web)
+#required 00000000-0000-0000-0000-000000000001 =
+# (for trh@r9-y3pll:~/bar)
+#required 357eaef4-af1b-491a-a003-01c2d583056e =
+
+# Scheduled activities
+# (Separate multiple activities with "; ")
+# (for web)
+#schedule 00000000-0000-0000-0000-000000000001 =
+# (for trh@r9-y3pll:~/bar)
+#schedule 357eaef4-af1b-491a-a003-01c2d583056e =
+</code></pre>