I think this effects all version control. I have a notebook that has been versioned under bzr for quite some time. After doing an system update (Ubuntu oneric) which pulled in 0.56 zim, the version control plugin is broken. It fails to detect the bzr repo and instead trys running git commands on my home directory. This happens to be under git control so it picks up that repository, which has no relation to the notebook! If I start to edit a page zim then tries to git add -A on $HOME. Which nearly locks the machine and I'm killing zim to stop it wrecking my home git repo.

Problem appears to be, as noted above, zim checking home rather than the notebook directory for a repo.

The note book is in ~/LabBook. Opening the versions diag under zim -D gives this:

 DEBUG: Action: show_versions
 INFO: Running: ['git', 'log', '--date=iso'] (cwd: /home/mda)
 DEBUG: Opening dialog "Versions - Zim"

Version info:

 mda@starbuck:~/LabBook$ zim --version
 zim 0.56
 ...
 
 mda@starbuck:~/LabBook$ git --version
 git version 1.7.5.4

 mda@starbuck:~/LabBook$ bzr --version
 Bazaar (bzr) 2.4.1
   Python interpreter: /usr/bin/python 2.7.2
   Python standard library: /usr/lib/python2.7
   Platform: Linux-3.0.0-22-generic-x86_64-with-Ubuntu-11.10-oneiric
   bzrlib: /usr/lib/python2.7/dist-packages/bzrlib
   Bazaar configuration: /home/mda/.bazaar
   Bazaar log file: /home/mda/.bzr.log
   ...
 
 mda@starbuck:~/LabBook$ lsb_release -a
 No LSB modules are available.
 Distributor ID:	Ubuntu
 Description:	Ubuntu 11.10
 Release:	11.10
 Codename:	oneiric

 mda@starbuck:~/LabBook$ uname -a
 Linux starbuck 3.0.0-22-generic #36-Ubuntu SMP Tue Jun 12 17:37:42 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux
 
Full log:

 mda@starbuck:~/LabBook$ DEBUG: Loading /home/mda/.config/zim/preferences.conf
 DEBUG: Gtk version is (2, 24, 6)
 DEBUG: Pygtk version is (2, 24, 0)
 WARNING: Could not find all icon sizes for the application icon
 DEBUG: Loading /home/mda/.config/zim/style.conf
 DEBUG: Accelmap: /home/mda/.config/zim/accelmap
 DEBUG: Opening notebook: file:///home/mda/LabBook
 DEBUG: Loading /home/mda/LabBook/notebook.zim
 DEBUG: Cache dir: /home/mda/LabBook/.zim
 DEBUG: Index database file: /home/mda/LabBook/.zim/index.db
 DEBUG: Loading /home/mda/LabBook/.zim/state.conf
 INFO: Accelerator changed for <Actions>/CalendarPlugin/go_page_today
 DEBUG: Loaded plugin calendar (<CalendarPlugin object at 0x1d66af0 (zim+plugins+PluginClass at 0x1c8aec0)>)
 DEBUG: Loaded plugin insertsymbol (<InsertSymbolPlugin object at 0x1d66cd0 (zim+plugins+PluginClass at 0x1c7bf20)>)
 INFO: Accelerator changed for <Actions>/PrintToBrowserPlugin/print_to_browser
 DEBUG: Loaded plugin printtobrowser (<PrintToBrowserPlugin object at 0x1d66dc0 (zim+plugins+PluginClass at 0x1c8ae20)>)
 INFO: Accelerator changed for <Actions>/SpellPlugin/toggle_spellcheck
 DEBUG: Loaded plugin spell (<SpellPlugin object at 0x1d72410 (zim+plugins+PluginClass at 0x1c8af20)>)
 DEBUG: Loaded plugin tags (<TagsPlugin object at 0x1d725a0 (zim+plugins+PluginClass at 0x1c8af00)>)
 DEBUG: Loaded plugin tasklist (<TaskListPlugin object at 0x1d72c80 (zim+plugins+tasklist+TaskListPlugin at 0x1c8d540)>)
 DEBUG: Sending to daemon: ["ping",[],{}]
 
 DEBUG: Daemon replied: "Ack"
 DEBUG: Sending to daemon: ["vivicate",["zim.plugins.trayicon.AppIndicatorTrayIcon","TrayIcon"],{}]
 
 DEBUG: Child spawned 7015 (u'zim.plugins.trayicon.AppIndicatorTrayIcon', u'TrayIcon')
 DEBUG: No such signal: notebook-list-changed
 DEBUG: Daemon replied: true
 DEBUG: Loaded plugin trayicon (<TrayIconPlugin object at 0x1fc36e0 (zim+plugins+PluginClass at 0x1c8f8c0)>)
 INFO: Accelerator changed for <Actions>/VersionControlPlugin/save_version
 INFO: VCS detected: <zim.plugins.versioncontrol.VCSBackend object at 0x1fee610>
 DEBUG: Loaded plugin versioncontrol (<VersionControlPlugin object at 0x1fd0910 (zim+plugins+PluginClass at 0x1c8f8e0)>)
 INFO: Starting async index update
 INFO: Open page: <FileStorePage: Calendar:2012:06:23> (<HistoryPath: Calendar:2012:06:23>)
 DEBUG: Sending to daemon: ["ping",[],{}]
 
 DEBUG: Daemon replied: "Ack"
 DEBUG: Wrote /home/mda/.config/zim/preferences.conf
 DEBUG: Action: set_pathbar_recent
 DEBUG: Loading /home/mda/LabBook/notebook.zim
 DEBUG: Action: toggle_sidepane
 DEBUG: Wrote /home/mda/.config/zim/notebooks.list
 DEBUG: Sending to daemon: ["list_objects",[],{}]
 
 DEBUG: Daemon replied: [["zim.gui.GtkInterface","file:///home/mda/LabBook"],["zim.plugins.trayicon.AppIndicatorTrayIcon","TrayIcon"]]
 DEBUG: Sending to daemon: ["connect_object",["notebook-list-changed",["zim.plugins.trayicon.AppIndicatorTrayIcon","TrayIcon"]],{}]
 
 DEBUG: Daemon replied: null
 WARNING: Could not find all icon sizes for the application icon
 INFO: Accelerator changed for <Actions>/VersionControlPlugin/show_versions
 INFO: Accelerator changed for <Actions>/CalendarPlugin/show_calendar
 INFO: Accelerator changed for <Actions>/TaskListPlugin/show_task_list
 INFO: Accelerator changed for <Actions>/InsertSymbolPlugin/insert_symbol
 INFO: Index update done
 DEBUG: Action: show_preferences
 DEBUG: Loading /usr/share/zim/applications/firefox.desktop
 DEBUG: Loading /usr/share/zim/applications/open.desktop
 DEBUG: Loading /usr/share/zim/applications/thunderbird.desktop
 DEBUG: Loading /usr/share/zim/applications/xdg-email.desktop
 DEBUG: Loading /usr/share/zim/applications/xdg-open.desktop
 DEBUG: Loading /usr/share/applications/opera-browser.desktop
 DEBUG: Loading /usr/share/applications/geany.desktop
 DEBUG: Loading /usr/share/applications/firefox.desktop
 DEBUG: Loading /usr/share/applications/chromium-browser.desktop
 WARNING: Failed to parse value for key "Name[bg]": Отваряне на нов прозорец в режим \"инкогнито\"
 DEBUG: Loading /usr/share/applications/kde4/kfmclient_html.desktop
 DEBUG: Loading /usr/share/applications/kompozer.desktop
 DEBUG: Loading /usr/share/applications/thunderbird.desktop
 DEBUG: Loading /usr/share/applications/abiword.desktop
 DEBUG: Loading /usr/share/zim/applications/firefox.desktop
 DEBUG: Loading /usr/share/zim/applications/open.desktop
 DEBUG: Loading /usr/share/zim/applications/thunderbird.desktop
 DEBUG: Loading /usr/share/zim/applications/xdg-email.desktop
 DEBUG: Loading /usr/share/zim/applications/xdg-open.desktop
 DEBUG: Loading /home/mda/.local/share/applications/wine-extension-txt.desktop
 DEBUG: Loading /usr/share/applications/mousepad.desktop
 DEBUG: Loading /usr/share/applications/geany.desktop
 DEBUG: Loading /usr/share/applications/gedit.desktop
 DEBUG: Loading /usr/share/applications/gvim.desktop
 DEBUG: Loading /usr/share/applications/abiword.desktop
 DEBUG: Loading /usr/share/zim/applications/firefox.desktop
 DEBUG: Loading /usr/share/zim/applications/open.desktop
 DEBUG: Loading /usr/share/zim/applications/thunderbird.desktop
 DEBUG: Loading /usr/share/zim/applications/xdg-email.desktop
 DEBUG: Loading /usr/share/zim/applications/xdg-open.desktop
 DEBUG: Loading /usr/share/zim/applications/firefox.desktop
 DEBUG: Loading /usr/share/zim/applications/open.desktop
 DEBUG: Loading /usr/share/zim/applications/thunderbird.desktop
 DEBUG: Loading /usr/share/zim/applications/xdg-email.desktop
 DEBUG: Loading /usr/share/zim/applications/xdg-open.desktop
 DEBUG: Loading description for "Arithmetic"
 DEBUG: Opening dialog "Preferences - Zim"
 DEBUG: Loading description for "Version Control"
 DEBUG: Opening dialog "Configure Plugin - Zim"
 DEBUG: Dialog response CANCEL
 DEBUG: Closed dialog "Configure Plugin"
 INFO: Spawning: ['/usr/bin/python', '/usr/bin/zim', '--manual', 'Plugins:Version Control'] (cwd: None)
 DEBUG: Process started with PID: 7033
 DEBUG: Child spawned 7034 (u'zim.gui.GtkInterface', u'file:///usr/share/zim/manual')
 DEBUG: Emitting signal: notebook-list-changed
 DEBUG: Sending to child 7015: ["on_notebook_list_changed",[],{}]
 
 DEBUG: Sending to child 7034: ["present",["Plugins:Version Control"],{"geometry":null,"fullscreen":null}]
 
 DEBUG: Loading /home/mda/LabBook/notebook.zim
 DEBUG: Wrote /home/mda/.config/zim/notebooks.list
 DEBUG: Sending to daemon: ["list_objects",[],{}]
 
 DEBUG: Daemon replied: [["zim.gui.GtkInterface","file:///home/mda/LabBook"],["zim.plugins.trayicon.AppIndicatorTrayIcon","TrayIcon"],["zim.gui.GtkInterface","file:///usr/share/zim/manual"]]
 DEBUG: Loading /usr/share/zim/manual/notebook.zim
 DEBUG: Loading /home/mda/.config/zim/preferences.conf
 DEBUG: Gtk version is (2, 24, 6)
 DEBUG: Pygtk version is (2, 24, 0)
 WARNING: Could not find all icon sizes for the application icon
 DEBUG: Loading /home/mda/.config/zim/style.conf
 DEBUG: Accelmap: /home/mda/.config/zim/accelmap
 DEBUG: Opening notebook: file:///usr/share/zim/manual
 DEBUG: Loading /usr/share/zim/manual/notebook.zim
 DEBUG: Cache dir: /home/mda/.cache/zim/notebook-usr_share_zim_manual
 DEBUG: Index database file: /home/mda/.cache/zim/notebook-usr_share_zim_manual/index.db
 INFO: Flushing index
 DEBUG: Loading /home/mda/.cache/zim/notebook-usr_share_zim_manual/state.conf
 INFO: Accelerator changed for <Actions>/CalendarPlugin/go_page_today
 DEBUG: Loaded plugin calendar (<CalendarPlugin object at 0x1da8c30 (zim+plugins+PluginClass at 0x1ccccc0)>)
 DEBUG: Loaded plugin insertsymbol (<InsertSymbolPlugin object at 0x1da8d70 (zim+plugins+PluginClass at 0x1cc1720)>)
 INFO: Accelerator changed for <Actions>/PrintToBrowserPlugin/print_to_browser
 DEBUG: Loaded plugin printtobrowser (<PrintToBrowserPlugin object at 0x1da8e60 (zim+plugins+PluginClass at 0x1cccc20)>)
 INFO: Accelerator changed for <Actions>/SpellPlugin/toggle_spellcheck
 DEBUG: Loaded plugin spell (<SpellPlugin object at 0x1da8f50 (zim+plugins+PluginClass at 0x1cccd20)>)
 DEBUG: Loaded plugin tags (<TagsPlugin object at 0x1dac140 (zim+plugins+PluginClass at 0x1cccd00)>)
 DEBUG: Loaded plugin tasklist (<TaskListPlugin object at 0x1dac5f0 (zim+plugins+tasklist+TaskListPlugin at 0x1ccd2c0)>)
 DEBUG: Sending to daemon: ["ping",[],{}]
 
 DEBUG: Daemon replied: "Ack"
 DEBUG: Sending to daemon: ["vivicate",["zim.plugins.trayicon.AppIndicatorTrayIcon","TrayIcon"],{}]
 
 DEBUG: Daemon replied: true
 DEBUG: Loaded plugin trayicon (<TrayIconPlugin object at 0x1dacaf0 (zim+plugins+PluginClass at 0x1ccd0e0)>)
 INFO: Accelerator changed for <Actions>/VersionControlPlugin/save_version
 INFO: No VCS detected
 DEBUG: Loaded plugin versioncontrol (<VersionControlPlugin object at 0x1db2d20 (zim+plugins+PluginClass at 0x1ccd0c0)>)
 INFO: Starting async index update
 INFO: Open page: <FileStorePage: Help:Wiki Syntax> (<HistoryPath: Help:Wiki Syntax>)
 DEBUG: Wrote /home/mda/.config/zim/preferences.conf
 DEBUG: Action: set_pathbar_recent
 DEBUG: Action: toggle_readonly
 INFO: Open page: <FileStorePage: Plugins:Version Control> (<Path: Plugins:Version Control>)
 INFO: Accelerator changed for <Actions>/VersionControlPlugin/show_versions
 INFO: Accelerator changed for <Actions>/CalendarPlugin/show_calendar
 INFO: Accelerator changed for <Actions>/TaskListPlugin/show_task_list
 INFO: Accelerator changed for <Actions>/InsertSymbolPlugin/insert_symbol
 DEBUG: Wrote /home/mda/.cache/zim/notebook-usr_share_zim_manual/state.conf
 INFO: Index update done
 DEBUG: Action: close (delete-event)
 DEBUG: Loading description for "Version Control"
 DEBUG: Opening dialog "Configure Plugin - Zim"
 DEBUG: Dialog response CANCEL
 DEBUG: Closed dialog "Configure Plugin"
 DEBUG: Dialog response OK
 DEBUG: Wrote /home/mda/.config/zim/style.conf
 DEBUG: Wrote /home/mda/.config/zim/preferences.conf
 DEBUG: Closed dialog "Preferences"
 mda@starbuck:~/LabBook$ DEBUG: Action: show_versions
 INFO: Running: ['git', 'log', '--date=iso'] (cwd: /home/mda)
 DEBUG: Opening dialog "Versions - Zim"