Fix broken links (#76)

aggregate-mappings.json

@@ -5,6 +5,7 @@
         "sda/cmd/intercept/intercept.md": "docs/services/intercept.md",
         "sda/cmd/mapper/mapper.md": "docs/services/mapper.md",
         "sda/cmd/verify/verify.md": "docs/services/verify.md",
+        "sda/cmd/s3inbox/s3inbox.md": "docs/services/s3inbox.md",
         "sda/sda.md": "docs/services/sda.md"
     }
 }

aggregate-repositories.sh

@@ -29,6 +29,11 @@ do
         fi
     done
 
+    # add special use case for sda.md links
+
+    sed -i -E 's#cmd\/(.+)\/#''#g' docs/services/sda.md
+    git add docs/services/sda.md
+
     # check if there are any changes
     if ! git status | grep 'nothing to commit'
     then

docs/CONTRIBUTING.md

@@ -67,7 +67,7 @@ Some tips about writing helpful commit messages:
  6. Wrap the body at 72 characters.
  7. Use the body to explain what and why vs. how.
 
-For an in-depth explanation of the above points, please see [How to Write a Git Commit Message](http://chris.beams.io/posts/git-commit/).
+For an in-depth explanation of the above points, please see [How to Write a Git Commit Message](https://chris.beams.io/posts/git-commit/).
 
 
 ### How we do code reviews

docs/services/sda.md

@@ -10,12 +10,12 @@ It can be used as part of a [Federated EGA](https://ega-archive.org/federated) o
 
 The SDA submission pipeline has four main steps:
 
-1. [Ingest](cmd/ingest/ingest.md) splits file headers from files, moving the header to the database and the file content to the archive storage.
-2. [Verify](cmd/verify/verify.md) verifies that the header is encrypted with the correct key, and that the checksums match the user-provided checksums.
-3. [Finalize](cmd/finalize/finalize.md) associates a stable accessionID with each archive file and backups the file.
-4. [Mapper](cmd/mapper/mapper.md) maps file accessionIDs to a datasetID.
+1. [Ingest](ingest.md) splits file headers from files, moving the header to the database and the file content to the archive storage.
+2. [Verify](verify.md) verifies that the header is encrypted with the correct key, and that the checksums match the user-provided checksums.
+3. [Finalize](finalize.md) associates a stable accessionID with each archive file and backups the file.
+4. [Mapper](mapper.md) maps file accessionIDs to a datasetID.
 
 There are also three additional support services:
 
-1. [Intercept](cmd/intercept/intercept.md) relays messages from `CentralEGA` to the system.
-2. [s3inbox](cmd/s3inbox/s3inbox.md) proxies uploads to the an S3 compatible storage backend.
+1. [Intercept](intercept.md) relays messages from `CentralEGA` to the system.
+2. [s3inbox](s3inbox.md) proxies uploads to the an S3 compatible storage backend.

docs/submission.md

@@ -131,7 +131,7 @@ Mina SSHD.
 
 > NOTE:
 > Sources are located at the separate repository:
-> <https://github.com/neicnordic/sensitive-data-archive/tree/main/sda-inbox-sftp> Essentially, it's a
+> <https://github.com/neicnordic/sensitive-data-archive/tree/main/sda-sftp-inbox> Essentially, it's a
 > Spring-based Maven project, integrated with the
 > [Local Message Broker](connection.md#local-message-broker).