@@ -15,15 +15,16 @@ the SD2E platform. Documentation for getting started with the SD2E API is below.
1515
1616  ;  ;  ;  ; 1.1 [ Request Access to the SD2E Platform] ( docs/request_access.md )
1717
18-   ;  ;  ;  ; 1.2 [ Install and Configure the CLI] ( docs/install_cli.md )
18+   ;  ;  ;  ; 1.2 [ Install and Configure the SD2E CLI] ( docs/install_cli.md )
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2020  ;  ;  ;  ; 1.3 [ Create the Client API Keys] ( docs/create_client.md )
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2222  ;  ;  ;  ; 1.4 [ Authorize with the SD2E Tenant] ( docs/authorization.md )
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2424  ;  ;  ;  ; 1.5 [ SSH Key Pairs] ( docs/ssh_keys.md )
2525
26-   ;  ; ** 2 Using the SD2E API**
26+
27+   ;  ; ** 2 Agave CLI Basics**
2728
2829  ;  ;  ;  ; 2.1 [ Storage and Execution System Basics] ( docs/systems_basics.md )
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@@ -35,26 +36,54 @@ the SD2E platform. Documentation for getting started with the SD2E API is below.
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3637  ;  ;  ;  ; 2.5 [ Prepare and Submit a Job] ( docs/submit_job.md )
3738
38-   ;  ; ** 3 Customizing the SD2E API**
39+   ;  ;  ;  ; 2.6 [ Create Private Systems] ( docs/create_systems.md )
40+
41+   ;  ;  ;  ; 2.7 [ Modify Existing Systems and Applications] ( docs/modify.md )
42+
43+   ;  ;  ;  ; 2.8 [ Advanced Job Control and Workflows] ( docs/advanced_job.md )
44+
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40-   ;  ;& nbsp ;& nbsp ; 3.1 [ Create Private Systems ] ( docs/create_systems.md )
46+   ;  ; ** 3 Agave Apps **
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42-   ;  ;  ;  ; 3.2 [ Create Custom Applications] ( docs/create_app.md )
48+   ;  ;  ;  ; 3.1 Create Custom Applications: Apps-Init (* coming soon* )
49+
50+   ;  ;  ;  ; 3.2 Deploy Custom Applications: Apps-Deploy (* coming soon* )
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4452  ;  ;  ;  ; 3.3 [ Share an Application with Others] ( docs/share_app.md )
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46-   ;  ;  ;  ; 3.4 [ Modify Existing Systems and Applications] ( docs/modify.md )
54+   ;  ;  ;  ; 3.4 Continuous Integration with Jenkins (* coming soon* )
55+
56+   ;  ;  ;  ; 3.5 [ Old App Building Process] ( docs/create_app.md ) (* Deprecated* )
57+
58+
59+   ;  ; ** 4 Abaco Reactors**
60+
61+   ;  ;  ;  ; 4.1 Abaco CLI Basics (* coming soon* )
62+
63+   ;  ;  ;  ; 4.2 Create Custom Reactors: Abaco Init (* coming soon* )
64+
65+   ;  ;  ;  ; 4.3 Deploy Custom Reactors: Abaco Deploy (* coming soon* )
66+
67+   ;  ;  ;  ; 4.4 Share a Reactor with Others (* coming soon* )
68+
69+   ;  ;  ;  ; 4.5 Continuous Integration with Jenkins (* coming soon* )
70+
71+   ;  ;  ;  ; 4.6 Automated Notifications and Message Passing (* coming soon* )
72+
73+
74+   ;  ; ** 5 Advanced SD2E Features**
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48-   ;  ; ** 4 Advanced SD2E Features **
76+   ;  ;& nbsp ;& nbsp ; 5.1 Agavepy ( * coming soon * )
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50-   ;  ;  ;  ; 4.1 [ Advanced Job Control and Workflows ] ( docs/advanced_job.md )
78+   ;  ;  ;  ; 5.2 AgaveDB ( * coming soon * )
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52-   ;  ;  ;  ; 4.2 Integration with Jupyter (* coming soon* )
80+   ;  ;  ;  ; 5.3 Jupyter Notebooks (* coming soon* )
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54-   ;  ;  ;  ; 4.3 Actor Based Containers ( * coming soon * )
82+   ;  ;  ;  ; 5.4 [ Singularity GPGPU Containers] ( docs/singularity_gpu_01.md )
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56-   ;  ;  ;  ; 4.4 [ Singularity GPGPU Containers] ( docs/singularity_gpu_01.md )
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85+   ;  ; ** 6 Placeholder**
86+   ;  ; ** 7 Reference Pages**
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