fixing broken links

Author: wjallen

docs/01.create_client.md

@@ -7,7 +7,7 @@ tagline:
 [The Agave API](http://developer.tacc.cloud/), (a component of the SD2E API), is
 used to configure your user environment to interact with the SD2E platform. If
 you do not yet have the CLI installed and in your `$PATH`, first go
-[here](01.02.install_cli.md) to install it.
+[here](01.install_cli.md) to install it.
 
 <br>
 #### Initiate with the SD2E Agave tenant

docs/01.ssh_keys.md

@@ -6,14 +6,14 @@ tagline:
 
 In certain circumstances, it is advantageous to use public / private SSH keys
 to authenticate with the Agave API. Specifically, this is important when
-[creating your own private systems](02.06.create_systems.md). Having SSH keys
+[creating your own private systems](02.create_systems.md). Having SSH keys
 will make it easier to interact with systems that do not allow password
 authentication or that require frequent password changes, and it will increase
 security by preventing the need to store your password in a plain text file.
 
 If you are new to the Agave CLI and the SD2E Agave tenant, it is recommended to
 skip this section of the documents until you need to
-[create your own private systems](02.06.create_systems.md).
+[create your own private systems](02.create_systems.md).
 
 <br>
 #### Prerequisites
@@ -76,7 +76,7 @@ Finally, add your public key to the `authorized_keys` file on your remote system
 [js-104-39] % cat agave_rsa.pub >> ~/.ssh/authorized_keys
 ```
 Your private key (`agave_rsa`) will be used in the future when it is time to
-[create your own private systems](02.06.create_systems.md). Never share your
+[create your own private systems](02.create_systems.md). Never share your
 private key with anyone else.
 
 

docs/02.create_systems.md

@@ -6,7 +6,7 @@ tagline:
 
 Most standard SD2E API users will not need to create custom execution or storage
 systems. By default, you have access to some private and public execution and
-storage systems that should connect you to [most of TACC resources](02.01.systems_basics.md).
+storage systems that should connect you to [most of TACC resources](02.systems_basics.md).
 
 Even so, there are circumstances where it is advantageous to create your own systems.
 For example, they can help you connect to private lab servers, license servers,
@@ -19,7 +19,7 @@ and execution system.
 
 For any system you register with Agave, you need the hostname and login credentials.
 The preferred login credentials are SSH key pairs. For instructions on creating
-appropriate public / private keys, see [here](01.05.ssh_keys.md).
+appropriate public / private keys, see [here](01.ssh_keys.md).
 
 You also need some basic information on the compute resources which will be
 registered as systems. For storage systems, you need to know the desired path
@@ -29,7 +29,7 @@ information about the queueing system (queue names, limits, etc.). For both type
 of execution system you need a path for running jobs.
 
 The Jetstream instance we will register has hostname `129.114.104.39`. We will
-assume the user '`username`' has already created [SSH keys](01.05.ssh_keys.md)
+assume the user '`username`' has already created [SSH keys](01.ssh_keys.md)
 and added the public key to `~/.ssh/known_hosts/`. The path for storing data
 will be the home directory, `/home/username/`. Since this instance does not have
 a queuing system, we will register it as a CLI execution system and run jobs

docs/02.data_management.mdd renamed to docs/02.data_management.md

@@ -10,7 +10,7 @@ list files, upload and download data, remotely manage and organize data, and imp
 external data from the web.
 
 Agave `files-*` commands act on Agave storage systems. See the
-[systems basics](02.01.systems_basics.md) documentation for more details.
+[systems basics](02.systems_basics.md) documentation for more details.
 
 This page is broken down into the following sections:
 
@@ -57,7 +57,7 @@ WARNING: The `files-delete` command will delete folders with or without contents
 
 *Tip: if you set `data-tacc-work-username` as your default system, then you
 do not need to provide it on the command line. More info
-[here](02.01.systems_basics.md).*
+[here](02.systems_basics.md).*
 
 <br>
 #### Uploading and downloading via the CLI
@@ -143,7 +143,7 @@ more descriptive information (when applicable) related to number of retries, per
 grants and revocations, reasons for failure, and hiccups that may have occurred in
 the transfer process.
 ```
-% files-history -S data-tacc-work-username sd2e-data/my_copy.txt                  
+% files-history -S data-tacc-work-username sd2e-data/my_copy.txt
 File item copied from https://api.sd2e.org/files/v2/media/system/data-tacc-work-username//sd2e-data/my_file.txt
 ```
 

docs/02.find_application.md

@@ -366,8 +366,8 @@ However, this is an important clue (along with the inputs, parameters, and app
 description) to indicate what is the function of this app.
 
 Once the appropriate app has been identified, the next steps are to
-[stage the input data](02.02.data_management.md), and to
-[prepare and submit a job](02.05.submit_job).
+[stage the input data](02.data_management.md), and to
+[prepare and submit a job](02.submit_job).
 
 ---
 Return to the [API Documentation Overview](../index.md)

docs/02.modify_systems.md

@@ -4,7 +4,7 @@ title: Modify Existing Systems
 tagline:
 ---
 
-Agave [systems](02.06.create_systems.md) are described by `json` files and added
+Agave [systems](02.create_systems.md) are described by `json` files and added
 to the SD2E tenant using the command line interface. To modify a system after it
 has been added, simply edit the original `json` file and use the command line
 interface to push the changes to the SD2E tenant.
@@ -14,7 +14,7 @@ interface to push the changes to the SD2E tenant.
 #### Modify an Agave system
 
 This is an example Agave storage system `json` file from an
-[earlier section](02.06.create_systems.md) of this user guide:
+[earlier section](02.create_systems.md) of this user guide:
 ```
 {
   "id": "jetstream-storage-username",

docs/02.submit_job.md

@@ -5,7 +5,7 @@ tagline:
 ---
 
 Continuing with the previous example of kallisto (see
-[Find an Application](02.04.find_application.md)), we know there are three
+[Find an Application](02.find_application.md)), we know there are three
 required input files, one required input parameter, and two optional input
 parameters for this specific application.
 
@@ -120,7 +120,7 @@ transcripts.fasta.gz
 Because this job had attribute `"archive":true` in the job template, the output
 files were archived in your `tacc-work` space under a folder named after your
 username. A copy of the output also remains in the jobs API space for easy access
-and, if desired, chaining into other jobs. The important output for this 
+and, if desired, chaining into other jobs. The important output for this
 particular job is all located in the `output` subdirectory.  Download just the
 `output` subdirectory using the following command:
 ```

docs/02.systems_basics.md

@@ -10,7 +10,7 @@ hostname. They may be public or private, and they may either be **storage** syst
 
 In SD2E, we provide all users with private storage and execution systems attached to
 TACC resources. If you would like to create your own systems attached to different
-resources, skip ahead to [Create Private Systems](02.06.create_systems.md).
+resources, skip ahead to [Create Private Systems](02.create_systems.md).
 
 
 <br>
@@ -257,7 +257,7 @@ information about queue types and availability.
 <br>
 #### Set a default system
 
-You may find that most of the [file operations](02.02.data_management.md) you
+You may find that most of the [file operations](02.data_management.md) you
 perform are against your private TACC storage system - `data-tacc-work-username`.
 To avoid typing the full name of the system with every file command, you may set
 it as the default system with:

docs/03.modify_applications.md

@@ -4,7 +4,7 @@ title: Modify Existing Systems and Applications
 tagline:
 ---
 
-Agave [systems](02.06.create_systems.md) and [apps](03.01.create_app.md) are described by
+Agave [systems](02.create_systems.md) and [apps](03.create_app.md) are described by
 `json` files and added to the SD2E tenant using the command line interface. To
 modify a system or app after it has been added, simply edit the original `json`
 file and use the command line interface to push the changes to the SD2E tenant.