Note: If you want any of this stuff in the actual release, please help add them here:
http://typewith.me/AnonOS-Development
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                                                        Stuff that hasn't been added
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http://www.i2p2.de/ Unfortunately, it has no RPM, so it's not that easy to add.
Bitcoin.
http://www.cypherpunk.at/onioncat/
http://listaller.nlinux.org/ (Cross-distro package installer. If you don't want to bother with RPMs or DEBs, try this. In alpha, though...)
http://klik.atekon.de/ (Application virtualization, portable, makes them run on any linux distro.)
http://0install.net/ Another portable application system, except that it runs on any system, windows, mac, and linux.
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                                        Programs that need to be made
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See this page for
Full-disk  encryption for a persistent drive, such as LUKS.
Samizdat Content Delivery system https://chiselapp.com/user/treeofsephiroth/repository/anonos/wiki?name=Atemoya
P2P update system, (Pre installed in Fedora, it's called Metalinks)

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                                                            Annonaceae:
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Window Manager
XVesa (for simple Hardware)
TWM (classical and  2D; works even on lowest-end-Hardware!)
Fluxbox (simple and elegant. Will work on the oldest of computers.)
remastersys
macchanger  – Scrambles MAC address to maintain anonymity in public wireless         networks
Libraries
Python – Python. Popular programming language.
Python-tkinter (python-tk) - ???
Perl – Programming swiss army knife.
OpenJDK – Java programming, open-source version.
Geany – Very simple and         usable multi-language programming tool. Able to compile things.
Flash Player – The web standard for rich multimedia content. (but HTML5!)
/* make optional as can break anonymity?*/
Actually, BetterPrivacy might make flashplayer ok. It destroys flash's super cookies. http://en.wikipedia.org/wiki/Local_Shared_Object
Still, i'll look into it.
Wine Compatibility Layer – For windows stuff.
Mono C# - For Windows stuff coded with .NET.
Components for Perl/C-C++ scripting, etc, so people can code their own stuff         (It's free software, after all)
Full-disk  encryption when installed, like TrueCrypt / ScamDisk
TruCrypt   will be more prone to issues but more flexible. On-ground activists   could access encrypted USB Keys from Windows using TrueCrypt. Consider   NOT putting anonOS itself into encryption. Adds overhead and provides  no  real benefit on a system that isn't intended to be persistant.  ramfs  might be better option. -Freeheart +1
You make a good point there.
apt-get and sypnatic
Internet
Tor
I2P
Osiris
Freenet?
ProxyChains– Proxies everything.
(possible vpns built in)
Firefox
Adobe Flash Plugin
Torbutton -
BetterPrivacy
(Additionally,   consider Tor IM and Browser Bundle, which ships with the above plus   Pidgin+OTR and is mostly pre-configured out of the tarball)
No, Linux doesn't have a Tor IM Bundle, only the browser. I prefer to configure it myself, anyway.
Ghostery -
noscript -
Defaulting Firefox settings to "Do not use JavaScript" might be better. JS can compromise identity.
(a free, fully automatic proxy system; maybe Anonymous-proxes?)
Siphon - (Add-On - Sync; http://siphon-fx.com/   ; recommered to preconfigure (monodirectional sync!), so that   AnonOS-Users can choose best Addons and get them installed with just  two  clicks each...)
We've   got it! To sync with AnonOS's add-on repo, install siphon, go to the   "tools" menu, then click add-ons, and then type this account:
username: mrmongler@hushmail.com
password: 0neAnon
Mozilla Add-on Collector -
AddonFox -
All-in-One Sidebar -
FoxyTunes (listen To AnonNewsRadio!)
BabelFish -
Do   we need translation plugins on a local system? They still require   internet and if the user has it, the web pages can be used. Saves space   and memory. Also browser agnostic. Instead provide bookmarks.
The space loss is very, very tiny. Still, i'll take your suggestion.
Greasemonkey -
NoRedirect -
AdBlock Plus -
Update Notifier -
Browser Masquerade - (and/or "Modify Headers")
Easy Youtube Video Downloader (Really important. Gets a local copy of a video in case Youtube takes it down.)
Consider http://bitbucket.org/rg3/youtube-dl/ instead. No browser dependency.
Cool.
Firefox Sync (I really don't think putting your info on a server is a good idea. Use siphon instead.)
Firebug -
FoxyProxy to manage proxies
Cookie Editor
and Tamper Data
FoxClocks (world time in the status bar)
SwitchHosts to edit the host files on-the-fly, with profiles
WOT (Web of Trust) -
Flagfox -
feedly -
HTTPS-Everywhere (??? Need link. Can't find it...)
/* https://www.eff.org/files/https-everywhere-latest.xpi ? */
Adblock Plus - (Easy, Fanboy lists)
NoScript -
YesScript - (inclued a blacklist for NoScript, so that it protects more sucsessful; still allows manual override trough users...)
BEEF TACO -
ReminderFox -
BetterPrivacy
Telify -
Certificate Patrol -
Personas -
Anonymous Personas
(see http://www.getpersonas.com/de/gallery/Designer/Netzblockierer )
jhead   (+other items that remove identifying metadata) – Sometimes, when   writing a public pdf, you could give away your name, and possibly   address. This, and other tools prevents that.
Encryption
wipe, shred, Secure-Delete suite – Deletes files so that they can never be recovered by adversaries
bleachbit - Wipes RAM to protect against cold boot attacks.
 Steganography tools – So you can hide code in a funny cat picture.
IRC
 BitchX – IRC bouncer, Client, and Server, all in one.
Irssi, xchat – Basic IRC  clients. No bouncing. Jbounce?
EPIC - WTF? it's a really awesome IRC, though.
xPDF (a small PDF reader!)
Abiword – Light word processing
Gnumeric – Light open-source spreadsheet
Twinkle,   SIP/ZRTP – VoIP phone that encrypts the connection, not as safe as  TOR,  but with macchanger, detection is extremely difficult. For  calling  people in a censored enviornment.
http://socialvpn.wordpress.com/   Holy crap, this one is awesome. Encrypted connections for a small  group  to share files and chat, and set up a private web server.
http://www.wippien.com/
VLC Media Player – Comes with every codec imaginable, plays anything you give it.
More Firefox addons (Or FIREKIPS to avoid copyright issues)
Frankly,   ignore copyright. The point here is to make a more effective tool for   activism. Respecting copyright and licenses might cripple anonymity   protection that is needed pre-boot but license-incompatible to ship in   binary. -Freeheart
k.
Puff V2.0 (WINE) – Use steganography on, well, anything.
GIMP – Powerful image processor, open-source photoshop.
Inkscape – SVG processor?
Guake – Makes opening terminals much, much quicker.
Conky – Displays information about the computer in a convenient, easy to reach         format.
Ubuntu Software Manager (Better package management than sypnatic)
Office
Thunderbird
Enigmail (GnuPG integration!)
Siphon
XML Digital Signature Processing Tool
Certificate PAtrol
Mozilla Add-on Collector
Sieve
Identity chooser
Display Mail User Agent
Update Notifier
ThunderBrowse
Personas
Anonymous Personas
GnuPG
(easy to use graphical interface!)
Ghostscript (create PDFs)
Sigil (ePub-Editor)
LibreOffice (openOffice is going to die out; free alternative!)
GIMP (for some Artwork-Creation ;-)
Inkscape (vector-drawing!)

Boot-Utils
Unetbootin / isolinux
DBAN (Darik's Boot and Nuke; a easy-to-use wiper!)
Console LOIC (The LOIC as a low-level-system; having ncruises-interace; including all the features form original!)
Copypasta (just insert AnonOS and an empty CD-R in Writer's tray and let it duplicate itself!)
Super Grub Disk (Repair MBR)
Inside Security (Virus Scan; Paritionating; lost of useful security/maintenance stuff)

Indigenous Packet Management
mountable Program Packages (examle; see: http://minisys-linux.de/muppy0083/index.htm ,
A   application system similar to Windows .EXE and Apple's DMG. Click it   and it just works, without needing to install on any distro. http://hacktolive.org/wiki/RUNZ
Tor Browser and IM Bundle covers a LOT of bases.
Not really. For linux, there is no Tor IM Bundle. And I prefer to have them integrated, there will be less leaks that way.
A p2p update system to prevent censorship and lessen the strain on each server. Apt-p2p would work wonders.
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                                    Cherimoya (Multipurpose Offensive/Defensive)
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Everything from CodeBase & Annonaceae
Complete Anonymous Starter Kit, to turn newfags into safe and powerful anons.
Includes stuff here: http://ge.tt/45p7kEz
And includes a guide to Programming in Python, Java, HTML, CSS, PHP, Javascript, and C++
Productive (only Installed on USB/HDD or SSD if wished! not in live-CD)
Apache – Quintessential web server.
Offensive suite:
AimSniff         – monitors         AIM/MSN messages across a server
Aircrack-NG - wireless offense and crack suite
MsgSnarf
Wireshark – Full-featured network sniffer
Ethercap GTK
Etherape
IM-Sniffer  – snoop on MSN/AIM/Email contacts.
Packet Injectors
Airpwn         – spoofs packets from a wireless network, effectively making YOU the server
Ettercap         - Ettercap           is a suite for man in the middle attacks on LAN. It features           sniffing of live connections, content filtering on the fly and   many         other interesting tricks.
Network Stress “testing”
 LOIC – Tests your “own”         servers against a DDOS attack
hping3         - TCP/IP packet assembler/analyzer
pyLOIC – Stress tester         that works behind TOR.
 HOIC – Multiple server         stress tester.
 Nessus – Network         vulnerablity scanner, useful for finding exploits “that you         immediately patch.”
Nikto, as a more user-friendly 'Nessus' -type pentest tool
Metasploit         - Comprehensive network testing tool. Uses every exploit imaginable         to test “your server’s” security.
 w3af         - Metasploit for the web. It finds exploits easily.
(possible wardialers, and free, anonymous VoIP)
Computer Security
 Ophcrack – grabs windows passwords
rainbowcrack -
John the Ripper -
Hydra – uses a dictionary attack to check for weak passwords, compatible with many network protocols
nmap – Maps out a entire network.
GOCR – Optical character recognition tool (for captchas?)
 (Add everything from BackTrack Linux, and from here: http://pastebin.com/f112b9f53

Features specific to Cherimoya
Bittorrent update/package system – Apt-p2p looks promising, and greatly reduces server strain.
AppArmor – restricts power of applications with profiles for greater security. SELinux for Fedora.
Must have a way to be put on a persistent USB flash drive. Call it AnarKeys or Boomstick.
Broadcom   43xx Support -  Current Ubuntu driver does not allow for packet   injection when breaking wireless encryption. Former driver is a pain in   the ass to find.
Icon set: Elementary – GNOME icon set, even looks better than Mac.
New  GTK Theme that is dark and easy on the eyes
Firefox  skin that turns it into FireKIPS (To avoid licensing issues)
404'ed  screen: Show “CAN'T LET YOU DO THAT, FIREFOX”.
Awesomeface menu button

Sprachenen>ca GoogleKE

More Firefox Addons
HackBar

Appearance Customizations:
http://piratenpad.de/AnonOS-artwork

Desktop-Shortcuts
Welcome to AnonOS!
Help
Office
Internet
Homepage (local; with dynamic stuff from external)
 (more here: http://piratepad.net/3540VLXFg7)
Anonymous eMail Poviders
http://www.privatedemail.net (german; servers in egypt)
http://hushmail.com
AnonOps: (http://www.anonops.ru)
WebChat (recommered for beginners or short session)
AnonNews http://anonnews.org/
JS-LOIC  http://pastehtml.com/view/1c9waaq.html
Censorship - Testing: http://www.herdict.org
AnonOS - Project
IRC-Chat (web)
Downloads

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                                            Atemoya (Virtual Appliance)
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(There should be no
Samizdat:

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http://www.furidamu.org/p2p-dns

http://socialvpn.wordpress.com/   Holy crap, this one is awesome. Encrypted connections for a small  group  to share files and chat, and set up a private web server.

http://www.typewith.me/the-web-we-need

http://map-of-power.blogspot.com/ Map of Power is a