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#1
When using in a Mozilla build system, it often advantageous to have jar.mn instead of chrome.manifest. Makefiles automatically pickup jar.mn and generate a .manifest file. In my case in Spicebird, the jar gets created smoothly and a newly created manifest file is placed along with in the chrome directory. I don't know how you are building the jar, but perhaps you could consider a jar.mn for your purpose too, since I think you are using the Mozilla build system in some manner anyway.

Here is my jar.mn file which is a bit incomplete for you:
minimizetotray.jar:
% content minimizetotray %chrome/content/
chrome/content/browser.js (chrome/content/browser.js)
chrome/content/browserOverlay.xul (chrome/content/browserOverlay.xul)
chrome/content/calendarOverlay.xul (chrome/content/calendarOverlay.xul)
chrome/content/calender.js (chrome/content/calender.js)
chrome/content/core.js (chrome/content/core.js)
chrome/content/collabOverlay.xul (chrome/content/collabOverlay.xul)
chrome/content/download.js (chrome/content/download.js)
chrome/content/downloadOverlay.xul (chrome/content/downloadOverlay.xul)
chrome/content/mail.js (chrome/content/mail.js)
chrome/content/mailOverlay.xul (chrome/content/mailOverlay.xul)
chrome/content/messengerOverlay.xul (chrome/content/messengerOverlay.xul)
chrome/content/minimizetotray.xul (chrome/content/minimizetotray.xul)
chrome/content/navigator.js (chrome/content/navigator.js)
chrome/content/navigatorOverlay.xul (chrome/content/navigatorOverlay.xul)
chrome/content/player.js (chrome/content/player.js)
chrome/content/playerOverlay.xul (chrome/content/playerOverlay.xul)
chrome/content/prefs-window.js (chrome/content/prefs-window.js)
chrome/content/prefs.xul (chrome/content/prefs.xul)
chrome/content/turboBrowser.js (chrome/content/turboBrowser.js)
chrome/content/turboBrowser.xul (chrome/content/turboBrowser.xul)
chrome/content/turbo.js (chrome/content/turbo.js)
chrome/content/turboNavigator.xul (chrome/content/turboNavigator.xul)

% skin minimizetotray classic/1.0 %chrome/skin/
chrome/skin/icon.png (chrome/skin/icon.png)
chrome/skin/icon.svg (chrome/skin/icon.svg)
chrome/skin/minimize-16.png (chrome/skin/minimize-16.png)
chrome/skin/minimize-24.png (chrome/skin/minimize-24.png)
chrome/skin/minimize-24.svg (chrome/skin/minimize-24.svg)
chrome/skin/minimize.svg (chrome/skin/minimize.svg)
chrome/skin/minimizetotray.css (chrome/skin/minimizetotray.css)

% locale minimizetotray ca-AD %chrome/locale/ca-AD/
#% locale minimizetotray cs-CZ %chrome/locale/cs-CZ/
% locale minimizetotray da-DK %chrome/locale/da-DK/
% locale minimizetotray de %chrome/locale/de/
% locale minimizetotray el-GR %chrome/locale/el-GR/
% locale minimizetotray en-US %chrome/locale/en-US/
% locale minimizetotray es-ES %chrome/locale/es-ES/
% locale minimizetotray et-EE %chrome/locale/et-EE/
#% locale minimizetotray eu-ES %chrome/locale/eu-ES/
#% locale minimizetotray fi-FI %chrome/locale/fi-FI/
% locale minimizetotray fr %chrome/locale/fr/
% locale minimizetotray fy-NL %chrome/locale/fy-NL/
% locale minimizetotray he-IL %chrome/locale/he-IL/
% locale minimizetotray hr-HR %chrome/locale/hr-HR/
% locale minimizetotray hu-HU %chrome/locale/hu-HU/
% locale minimizetotray is-IS %chrome/locale/is-IS/
% locale minimizetotray it-IT %chrome/locale/it-IT/
% locale minimizetotray ja %chrome/locale/ja/
% locale minimizetotray ko-KR %chrome/locale/ko-KR/
% locale minimizetotray lt-LT %chrome/locale/lt-LT/
% locale minimizetotray mk-MK %chrome/locale/mk-MK/
#% locale minimizetotray nb-NO %chrome/locale/nb-NO/
% locale minimizetotray nl %chrome/locale/nl/
% locale minimizetotray pl-PL %chrome/locale/pl-PL/
% locale minimizetotray pt-BR %chrome/locale/pt-BR/
% locale minimizetotray pt-PT %chrome/locale/pt-PT/
% locale minimizetotray ro-RO %chrome/locale/ro-RO/
% locale minimizetotray ru-RU %chrome/locale/ru-RU/
% locale minimizetotray si-LK %chrome/locale/si-LK/
% locale minimizetotray sk-SK %chrome/locale/sk-SK/
#% locale minimizetotray sl-SL %chrome/locale/sl-SL/
% locale minimizetotray sr-RS %chrome/locale/sr-RS/
% locale minimizetotray sv-SE %chrome/locale/sv-SE/
% locale minimizetotray vi-VN %chrome/locale/vi-VN/
% locale minimizetotray zh-CN %chrome/locale/zh-CN/
% locale minimizetotray zh-TW %chrome/locale/zh-TW/
chrome/locale/ca-AD/common.dtd (chrome/locale/ca-AD/common.dtd)
chrome/locale/ca-AD/common.properties (chrome/locale/ca-AD/common.properties)
chrome/locale/ca-AD/prefs-window.dtd (chrome/locale/ca-AD/prefs-window.dtd)
chrome/locale/cs-CZ/common.dtd (chrome/locale/cs-CZ/common.dtd)
chrome/locale/cs-CZ/common.properties (chrome/locale/cs-CZ/common.properties)
chrome/locale/cs-CZ/prefs-window.dtd (chrome/locale/cs-CZ/prefs-window.dtd)
chrome/locale/da-DK/common.dtd (chrome/locale/da-DK/common.dtd)
chrome/locale/da-DK/common.properties (chrome/locale/da-DK/common.properties)
chrome/locale/da-DK/prefs-window.dtd (chrome/locale/da-DK/prefs-window.dtd)
chrome/locale/de/common.dtd (chrome/locale/de/common.dtd)
chrome/locale/de/common.properties (chrome/locale/de/common.properties)
chrome/locale/de/prefs-window.dtd (chrome/locale/de/prefs-window.dtd)
chrome/locale/el-GR/common.dtd (chrome/locale/el-GR/common.dtd)
chrome/locale/el-GR/common.properties (chrome/locale/el-GR/common.properties)
chrome/locale/el-GR/prefs-window.dtd (chrome/locale/el-GR/prefs-window.dtd)
chrome/locale/en-US/common.dtd (chrome/locale/en-US/common.dtd)
chrome/locale/en-US/common.properties (chrome/locale/en-US/common.properties)
chrome/locale/en-US/prefs-window.dtd (chrome/locale/en-US/prefs-window.dtd)
chrome/locale/es-ES/common.dtd (chrome/locale/es-ES/common.dtd)
chrome/locale/es-ES/common.properties (chrome/locale/es-ES/common.properties)
chrome/locale/es-ES/prefs-window.dtd (chrome/locale/es-ES/prefs-window.dtd)
chrome/locale/et-EE/common.dtd (chrome/locale/et-EE/common.dtd)
chrome/locale/et-EE/common.properties (chrome/locale/et-EE/common.properties)
chrome/locale/et-EE/prefs-window.dtd (chrome/locale/et-EE/prefs-window.dtd)
chrome/locale/eu-ES/common.dtd (chrome/locale/eu-ES/common.dtd)
chrome/locale/eu-ES/common.properties (chrome/locale/eu-ES/common.properties)
chrome/locale/eu-ES/prefs-window.dtd (chrome/locale/eu-ES/prefs-window.dtd)
chrome/locale/fi-FI/common.dtd (chrome/locale/fi-FI/common.dtd)
chrome/locale/fi-FI/common.properties (chrome/locale/fi-FI/common.properties)
chrome/locale/fi-FI/prefs-window.dtd (chrome/locale/fi-FI/prefs-window.dtd)
chrome/locale/fr/common.dtd (chrome/locale/fr/common.dtd)
chrome/locale/fr/common.properties (chrome/locale/fr/common.properties)
chrome/locale/fr/prefs-window.dtd (chrome/locale/fr/prefs-window.dtd)
chrome/locale/fy-NL/common.dtd (chrome/locale/fy-NL/common.dtd)
chrome/locale/fy-NL/common.properties (chrome/locale/fy-NL/common.properties)
chrome/locale/fy-NL/prefs-window.dtd (chrome/locale/fy-NL/prefs-window.dtd)
chrome/locale/he-IL/common.dtd (chrome/locale/he-IL/common.dtd)
chrome/locale/he-IL/common.properties (chrome/locale/he-IL/common.properties)
chrome/locale/he-IL/prefs-window.dtd (chrome/locale/he-IL/prefs-window.dtd)
chrome/locale/hr-HR/common.dtd (chrome/locale/hr-HR/common.dtd)
chrome/locale/hr-HR/common.properties (chrome/locale/hr-HR/common.properties)
chrome/locale/hr-HR/prefs-window.dtd (chrome/locale/hr-HR/prefs-window.dtd)
chrome/locale/hu-HU/common.dtd (chrome/locale/hu-HU/common.dtd)
chrome/locale/hu-HU/common.properties (chrome/locale/hu-HU/common.properties)
chrome/locale/hu-HU/prefs-window.dtd (chrome/locale/hu-HU/prefs-window.dtd)
chrome/locale/is-IS/common.dtd (chrome/locale/is-IS/common.dtd)
chrome/locale/is-IS/common.properties (chrome/locale/is-IS/common.properties)
chrome/locale/is-IS/prefs-window.dtd (chrome/locale/is-IS/prefs-window.dtd)
chrome/locale/it-IT/common.dtd (chrome/locale/it-IT/common.dtd)
chrome/locale/it-IT/common.properties (chrome/locale/it-IT/common.properties)
chrome/locale/it-IT/prefs-window.dtd (chrome/locale/it-IT/prefs-window.dtd)
chrome/locale/ja/common.dtd (chrome/locale/ja/common.dtd)
chrome/locale/ja/common.properties (chrome/locale/ja/common.properties)
chrome/locale/ja/prefs-window.dtd (chrome/locale/ja/prefs-window.dtd)
chrome/locale/ko-KR/common.dtd (chrome/locale/ko-KR/common.dtd)
chrome/locale/ko-KR/common.properties (chrome/locale/ko-KR/common.properties)
chrome/locale/ko-KR/prefs-window.dtd (chrome/locale/ko-KR/prefs-window.dtd)
chrome/locale/lt-LT/common.dtd (chrome/locale/lt-LT/common.dtd)
chrome/locale/lt-LT/common.properties (chrome/locale/lt-LT/common.properties)
chrome/locale/lt-LT/prefs-window.dtd (chrome/locale/lt-LT/prefs-window.dtd)
chrome/locale/mk-MK/common.dtd (chrome/locale/mk-MK/common.dtd)
chrome/locale/mk-MK/common.properties (chrome/locale/mk-MK/common.properties)
chrome/locale/mk-MK/prefs-window.dtd (chrome/locale/mk-MK/prefs-window.dtd)
chrome/locale/nb-NO/common.dtd (chrome/locale/nb-NO/common.dtd)
chrome/locale/nb-NO/common.properties (chrome/locale/nb-NO/common.properties)
chrome/locale/nb-NO/prefs-window.dtd (chrome/locale/nb-NO/prefs-window.dtd)
chrome/locale/nl/common.dtd (chrome/locale/nl/common.dtd)
chrome/locale/nl/common.properties (chrome/locale/nl/common.properties)
chrome/locale/nl/prefs-window.dtd (chrome/locale/nl/prefs-window.dtd)
chrome/locale/pl-PL/common.dtd (chrome/locale/pl-PL/common.dtd)
chrome/locale/pl-PL/common.properties (chrome/locale/pl-PL/common.properties)
chrome/locale/pl-PL/prefs-window.dtd (chrome/locale/pl-PL/prefs-window.dtd)
chrome/locale/pt-BR/common.dtd (chrome/locale/pt-BR/common.dtd)
chrome/locale/pt-BR/common.properties (chrome/locale/pt-BR/common.properties)
chrome/locale/pt-BR/prefs-window.dtd (chrome/locale/pt-BR/prefs-window.dtd)
chrome/locale/pt-PT/common.dtd (chrome/locale/pt-PT/common.dtd)
chrome/locale/pt-PT/common.properties (chrome/locale/pt-PT/common.properties)
chrome/locale/pt-PT/prefs-window.dtd (chrome/locale/pt-PT/prefs-window.dtd)
chrome/locale/ro-RO/common.dtd (chrome/locale/ro-RO/common.dtd)
chrome/locale/ro-RO/common.properties (chrome/locale/ro-RO/common.properties)
chrome/locale/ro-RO/prefs-window.dtd (chrome/locale/ro-RO/prefs-window.dtd)
chrome/locale/ru-RU/common.dtd (chrome/locale/ru-RU/common.dtd)
chrome/locale/ru-RU/common.properties (chrome/locale/ru-RU/common.properties)
chrome/locale/ru-RU/prefs-window.dtd (chrome/locale/ru-RU/prefs-window.dtd)
chrome/locale/si-LK/common.dtd (chrome/locale/si-LK/common.dtd)
chrome/locale/si-LK/common.properties (chrome/locale/si-LK/common.properties)
chrome/locale/si-LK/prefs-window.dtd (chrome/locale/si-LK/prefs-window.dtd)
chrome/locale/sk-SK/common.dtd (chrome/locale/sk-SK/common.dtd)
chrome/locale/sk-SK/common.properties (chrome/locale/sk-SK/common.properties)
chrome/locale/sk-SK/prefs-window.dtd (chrome/locale/sk-SK/prefs-window.dtd)
chrome/locale/sl-SL/common.dtd (chrome/locale/sl-SL/common.dtd)
chrome/locale/sl-SL/common.properties (chrome/locale/sl-SL/common.properties)
chrome/locale/sl-SL/prefs-window.dtd (chrome/locale/sl-SL/prefs-window.dtd)
chrome/locale/sr-RS/common.dtd (chrome/locale/sr-RS/common.dtd)
chrome/locale/sr-RS/common.properties (chrome/locale/sr-RS/common.properties)
chrome/locale/sr-RS/prefs-window.dtd (chrome/locale/sr-RS/prefs-window.dtd)
chrome/locale/sv-SE/common.dtd (chrome/locale/sv-SE/common.dtd)
chrome/locale/sv-SE/common.properties (chrome/locale/sv-SE/common.properties)
chrome/locale/sv-SE/prefs-window.dtd (chrome/locale/sv-SE/prefs-window.dtd)
chrome/locale/vi-VN/common.dtd (chrome/locale/vi-VN/common.dtd)
chrome/locale/vi-VN/common.properties (chrome/locale/vi-VN/common.properties)
chrome/locale/vi-VN/prefs-window.dtd (chrome/locale/vi-VN/prefs-window.dtd)
chrome/locale/zh-CN/common.dtd (chrome/locale/zh-CN/common.dtd)
chrome/locale/zh-CN/common.properties (chrome/locale/zh-CN/common.properties)
chrome/locale/zh-CN/prefs-window.dtd (chrome/locale/zh-CN/prefs-window.dtd)
chrome/locale/zh-TW/common.dtd (chrome/locale/zh-TW/common.dtd)
chrome/locale/zh-TW/common.properties (chrome/locale/zh-TW/common.properties)
chrome/locale/zh-TW/prefs-window.dtd (chrome/locale/zh-TW/prefs-window.dtd)

% overlay chrome://collab/content/collab.xul chrome://minimizetotray/content/collabOverlay.xul
% overlay chrome://collab/content/collab.xul chrome://minimizetotray/content/minimizetotray.xul
% override chrome://minimizetotray/locale/brand.dtd chrome://branding/locale/brand.dtd
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#2
I sometimes use the build system to create the binary. Other times I use things like VS and Eclipse. It is all a bit chaotic, and I need to get my act together.

I will try and work though all the patches you have sent once I get sometime to do so, UNI starts on Monday so I might be a little busy for awhile. They are git patches, so I hope that causes no problems with me using SVN.

A huge thanks for all the work you have put in! I really do appreciate it and I hope a learn a fair be of them, as some look very interesting.

Have I helped you? Do you like my add-ons?
Would you consider donating to show your appreciation for my efforts?

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