Issue 1:
We've been collecting data on which packages have deprecations since 0.201. This is a list of the packages using deprecated APIs, their owners and each package's impact. This data reflects a subset of the user population (those who have upgraded to 201). Affected numbers are based on unique users catching the deprecations.

If you are a maintainer on this list please note that we will be removing deprecated APIs on June 1st. See the blog post for more info. Note that upgrading to the new APIs will decrease breakage, increase speed, and generally be better for everyone.

Upgrading your package

We have a few guides for upgrading your package or theme:

Upgrading your package

Upgrading your package styles or UI theme

Upgrading your syntax theme

If you do only one thing, use atom-space-pen-views for the View class rather than importing them from atom. See the package upgrade guide for details.

Not sure what deprecations your package is generating? See https://gist.github.com/benogle/6d09e295c84b717ef9b4 for a list

Need help upgrading?

The community and the core team can offer some help:

Post an issue on the forum

Get help in the slack room

If you're stuck, post an issue on atom/atom

Package abandoned?

If your package is abandoned or supplanted by something in core, please comment with the package name and we can take steps to remove it from the package listing and people's install.

However, _do not delete the package repo from GitHub before unpublishing_, as this will make it so that you can't unpublish from the package registry.

Notes

We are currently working on ways to minimize pain from deprecations. We will try hard to keep things going smoothly through the transition

It appears there are many many people still using outdated packages. We have taken steps in v0.200 to be more aggressive about upgrading packages.

If you want to tinker with the data, it is all here: https://github.com/benogle/deprecation-data

Generated: Wed Jun 03 2015 18:15:00 GMT-0700 (PDT)

n
Package
Owner
Total Affected
Affected On Latest

1
file-types
@execjosh
20670
0.3.0 : 20670

2
auto-indent
@griiin
19527
0.1.0 : 19527

3
fancy-new-file
@rev087
14661
0.7.0 : 14661

4
tab-history
@guillaume86
13499
0.4.0 : 13499

5
atom-rails
@tomkadwill
12921
0.4.0 : 12891

6
auto-update-packages
@yujinakayama
11173
0.2.2 : 11173

7
filetype-color
@sommerper
10927
0.1.4 : 10822

8
web-view
@gabceb
9876
0.3.0 : 9756

9
ionic-atom
@RokkinCat
8678
0.3.1 : 8678

10
jsdoc
@craig-o
8676
0.9.0 : 8646

11
comment
@havber
8297
0.2.7 : 8297

12
rspec
@fcoury
8995
0.3.0 : 8083

13
highlight-css-color
@wonnage
7913
1.3.0 : 7913

14
symbol-gen
@weskinner
7686
0.3.0 : 7458

15
html2jade
@mirek
6499
0.7.0 : 6469

16
recent-projects
@Exter-N
6359
0.3.0 : 6359

17
local-history
@Nicolab
6928
3.1.0 : 6072

18
language-javascript-semantic
@p-e-w
5906
0.1.0 : 5906

19
sassbeautify
@badsyntax
5071
0.2.0 : 5071

20
html-helper
@j4ys0n
5054
0.2.3 : 5054

21
minifier
@wylst
4899
0.2.0 : 4809

22
virtualenv
@jhutchins
4746
0.6.2 : 4746

23
html-img
@minodisk
4715
0.4.0 : 4505

24
rails-navigation
@strikingcode
4503
0.1.1 : 4458

25
eslint
@iancmyers
4444
0.15.0 : 4444

26
yosemite-unity-ui
@k9ordon
4035
0.3.13 : 4035

27
term
@tjmehta
3840
0.2.2 : 3840

28
localization
@pandarison
3516
1.16.1 : 3516

29
atom-spotify
@jakemarsh
3258
1.2.0 : 3258

30
closure-linter
@miaopeng
3149
0.2.5 : 3149

31
omni-ruler
@Problematic
2939
0.3.1 : 2939

32
max-tabs
@klorenz
2877
0.3.0 : 2877

33
csscomb
@bruce
2738
0.1.2 : 2738

34
cucumber-runner
@gaslight
2733
0.1.1 : 2733

35
tree-view
@atom
2722
0.172.0 : 2557

36
execute-as-ruby
@torsten
2496
0.1.1 : 2496

37
livereload
@taggon
2422
0.2.0 : 2422

38
gradle-ci
@florianb
2411
0.2.3 : 2411

39
cucumber-step
@gaslight
2406
0.1.2 : 2406

40
python-coverage
@sueastside
2361
0.2.0 : 2361

41
browser-refresh
@raviraa
3166
0.8.3 : 2312

42
error-status
@postcasio
2300
0.3.3 : 2300

43
layout-manager
@santip
2191
0.2.3 : 2191

44
select-scope
@wmadden
2160
0.2.0 : 2160

45
r-exec
@hafen
2036
0.1.0 : 2036

46
function-name-in-status-bar
@francodacosta
1858
0.2.6 : 1858

47
atom-beautifier
@anaptfox
1827
0.5.0 : 1827

48
true-color
@captainwz
1812
0.4.1 : 1812

49
maximize-panes
@santip
1690
0.1.0 : 1690

50
gocode
@typester
1596
0.2.1 : 1596

51
ruby-strftime-reference
@cannikin
1582
0.3.0 : 1522

52
github-issues
@baconscript
1737
0.5.0 : 1497

53
rest-client
@ddavison
1461
0.3.3 : 1461

54
hipster-ipsum
@kristenmills
1324
0.1.0 : 1324

55
atom-browser-webview
@gstack
1308
0.6.0 : 1308

56
expand-selection
@mrolla
1246
0.2.1 : 1246

57
autocomplete-plus-jedi
@fallenhitokiri
1188
0.0.9 : 1188

58
pepper-autocomplete
@TonkWorks
1109
0.6.0 : 1109

59
big-cursor
@chick-chains
1096
0.1.0 : 1096

60
status-tab-spacing
@roe
1095
0.3.1 : 1095

61
erb-snippets
@MartinPeverelli
1263
0.5.0 : 1081

62
quick-move-file
@benastan
1080
0.7.0 : 1080

63
markdown-helpers
@catacgc
1125
0.2.2 : 1035

64
sloc
@sgade
1020
0.1.3 : 1020

65
runcoderun
@jgarth
1002
0.5.1 : 1002

66
line-count
@mark-hahn
1293
0.3.3 : 989

67
enhanced-tabs
@js-padavan
974
1.1.0 : 974

68
timekeeper
@skulled
959
0.4.0 : 959

69
indentation-jumper
@7even
958
0.1.1 : 958

70
rsense
@rsense
914
0.6.0 : 914

71
codeship-status
@codeship
912
0.1.1 : 912

72
devdocs
@masnun
821
0.2.0 : 821

73
mocha
@jerp
792
0.0.5 : 792

74
go-to-view
@mgbatchelor
791
0.1.2 : 791

75
swift-playground
@tachiba
761
0.2.0 : 761

76
paredit
@MarcoPolo
732
1.0.0 : 732

77
markdown-stream
@kenokabe
732
0.6.0 : 732

78
firepad
@firebase
714
0.3.1 : 714

79
space-block-jumper
@aronj
685
0.4.3 : 685

80
word-count
@Problematic
670
0.1.0 : 670

81
voicecode
@VoiceCode
715
0.9.0 : 670

82
mechanical-keyboard
@remanc
670
0.1.0 : 670

83
emacs-mode
@fuqcool
657
0.0.29 : 657

84
slash-closer
@postcasio
639
0.7.1 : 639

85
atom-raml-preview
@cybertk
639
0.0.1 : 639

86
asteroids
@mojombo
638
0.2.0 : 638

87
atom-2048
@void-main
623
1.2.3 : 623

88
spark-dfu-util
@suda
608
0.4.0 : 608

89
easy-motion
@adrian-budau
638
1.1.4 : 608

90
eval
@ardcore
608
0.2.0 : 608

91
atom-ungit
@codingtwinky
606
0.4.3 : 606

92
mark-ring
@jhonaker
578
3.0.0 : 578

93
custom-title
@postcasio
578
0.7.1 : 578

94
increment-number
@dsuket
548
0.1.0 : 548

95
supercopair
@deusanyjunior
546
0.9.34 : 546

96
pane-layout-switcher
@leny
608
0.0.3 : 532

97
path
@weskinner
438
0.4.1 : 438

98
atom-html5-boilerplate
@Snake231088
410
0.2.0 : 410

99
atom-htmlizer
@webBoxio
410
0.1.1 : 410

100
git-review
@wenlock
409
0.2.1 : 409

101
local-server
@lohek
396
0.1.0 : 396

102
open-in-gitx
@nfo
396
0.1.1 : 396

103
atom-python-debugger
@fxdgear
2528
0.3.0 : 395

104
atom-grunt-configs
@creynders
380
0.1.0 : 380

105
icon-font-picker
@travs
441
0.0.2 : 365

106
ruby-hash-rocket
@erbmicha
336
1.1.2 : 336

107
atom-faker
@manuclementz
335
0.2.0 : 335

108
atomic-rest
@lzrski
333
0.2.1 : 333

109
auto-replace-in-selection
@Kraoz
320
2.1.0 : 320

110
composer
@alairock
305
0.3.1 : 305

111
explicit-reload
@131
304
0.2.0 : 304

112
keycodes
@nickstark
304
0.1.2 : 304

113
package-list-downloader
@Trudko
303
0.2.1 : 303

114
asciidoc-preview
@asciidoctor
442
0.5.0 : 289

115
highlight-cov
@benjamine
288
0.1.0 : 288

116
atom-semicolons
@balupton
274
0.1.5 : 274

117
permute
@kristenmills
259
0.1.0 : 259

118
run-file
@alexand7u
258
0.9.0 : 258

119
coffee-trace
@mark-hahn
243
0.2.2 : 243

120
kinetic
@ddavison
213
0.2.5 : 213

121
webview-pane
@mizchi
213
0.0.1 : 213

122
floobits
@Floobits
197
0.4.2 : 197

123
playlist
@dreid93
195
0.1.7 : 195

124
ruler
@iambald
184
0.2.3 : 184

125
inc-dec-value
@leny
244
0.0.7 : 183

126
clipboard-history
@unDemian
501
0.6.5 : 182

127
assign-align
@leejarvis
167
0.1.0 : 167

128
ti-alloy-related
@soulglo
304
0.8.0 : 138

129
gitter
@Glavin001
135
0.6.2 : 135

130
save-commands
@JsonHunt
107
0.6.1 : 107

131
turnip-step
@hanachin
105
1.0.0 : 105

132
support-gbk
@ibigbug
105
1.1.0 : 105

133
related-files
@raviraa
92
0.3.0 : 92

134
coverage
@philipgiuliani
181
0.6.0 : 91

135
npm-autocomplete
@capaj
91
0.1.2 : 91

136
tab-switcher
@oggy
90
0.2.0 : 90

137
laravel-facades
@RyanNielson
76
1.0.0 : 76

138
clone-cursor
@thislooksfun
76
1.0.0 : 76

139
yuno-commit
@suda
75
0.0.2 : 75

140
change-case
@robhurring
76
0.5.1 : 61

141
marked
@cliffrowley
394
0.1.8 : 60

142
weather-package
@gladimdim
60
1.5.4 : 60

143
php-server
@leijou
60
0.4.0 : 60

144
toggle-tabs
@chadmoore
60
0.1.8 : 60

145
atom-charcode
@ka-ka-xyz
46
0.4.0 : 46

146
lorem-ipsum
@nickclaw
2510
0.5.0 : 45

147
vnc
@sidorares
45
0.1.3 : 45

148
php-documentation-online
@pi-coder
45
0.2.1 : 45

149
party-hard
@noraesae
45
0.3.3 : 45

150
convert-to-utf8
@dongri
75
0.1.0 : 45

151
pair-programming
@PierreVannier
45
0.7.0 : 45

152
angularjs-helper
@orlaqp
228
0.9.2 : 45

153
atom-html-preview
@webBoxio
2631
0.1.6 : 30

154
atom-prettify
@adambutler
365
0.1.1 : 30

155
view-tail-large-files
@mark-hahn
1608
0.1.17 : 30

156
preview-plus
@skandasoft
180
1.1.42 : 30

157
open-in-sourcetree
@cliffrowley
274
0.1.3 : 30

158
synced-sidebar
@peterdotjs
30
0.2.3 : 30

159
markdown-writer
@zhuochun
137
1.3.2 : 15

160
open-git-modified-files
@hmatsuda
15
0.1.0 : 15

161
open-in-github-app
@cliffrowley
167
0.2.3 : 15

162
project-ring
@vellerefond
300
0.20.5 : 15

163
import
@ezhilvendhan
227
1.3.0 : 15

164
atom-processing
@verytired
15
0.1.0 : 15

165
gitignore-snippets
@jefkoslowski
288
0.2.3 : 15

166
gulp-helper
@kenwheeler
364
4.1.0 : 15

167
atom-cli-diff
@mafiuss
75
0.11.0 : 15

168
apex-ui-personalize
@gstack
15
0.1.0 : 15

169
mdurl
@hemanth
15
0.2.0 : 15

170
php-getters-setters
@francodacosta
5098
0.5.0 : 15

171
elixir-cmd
@jerp
165
0.2.6 : 15

172
get-routes
@Levia
75
0.2.0 : 15

Issue 2:
Making Ctrl+Shift+s into save-all. I noticed that if I changed int under keymaps.cson (the suggested method) the keymaps would overload, not override the default save-as. This means that when I do the command both actions take place, which is not what I intended to do. I wanted it to only execute the save-all instead of save-as ot both.

If I change it in the local keymap.json it works fine but every time I update atom the change gets reset to default. Which is pretty annoying having to do every update. If there is a fix let me know.

Atom v0.136.0

Win 7