add links

src/outputs.md

@@ -86,7 +86,7 @@ datasets.
 When generated, an execution report that completely describes the processing
 that was executed and the dataset MUST comply with the BIDS Provenance Extension
 Proposal (BEP28). These outputs are OPTIONAL, and if provided, should be
-specified in the `output-files` section of the tool descriptor.
+specified in the [`output-files`](./outputs.md) of the tool descriptor.
 
 Similarly, the dataset_description.json file SHOULD be updated to reflect the
 processing that has occurred by the BIDS Application.

src/scope.md

@@ -38,7 +38,7 @@ which were described in Gorgolewski, et al. 2017
 (doi:[10.1371/journal.pcbi.1005209](https://doi.org/10.1371/journal.pcbi.1005209)),
 here referred to as BIDS-Apps 1.0. Backwards compatibility with BIDS-Apps 1.0 is
 not an explicit goal, but can be achieved in many cases as is discussed in
-Section [3.1.2.1](#3-1-2-1-backwards-compatibility-9). A summary of changes from
+the section [on backwards-compatibility](./inputs#backwards-compatibility). A summary of changes from
 BIDS-Apps 1.0 is included in the [CHANGELOG](./CHANGELOG.md#0.1.0.dev).
 
 This specification is seen as complementary to BIDS-Derivatives, which is part

src/specification.md

@@ -6,15 +6,15 @@ There are three domains of requirements that BIDS Applications must specify:
 1.  Required application behaviors
 1.  Required application outputs
 
-BIDS contains "required", "recommended" and "optional" fields. These are
-indicated throughout the document:
+BIDS contains "required", "recommended" and "optional" fields.
+These are indicated throughout the document:
 
 -   **REQUIRED**: essential to be BIDS compliant (meaning MUST as per RFC2199)
 -   **RECOMMENDED**: gives a warning if not present (meaning SHOULD as per RFC2199)
 -   **OPTIONAL**: no warning if missing (meaning MAY as per RFC2199)
 
-Ultimately, through using Boutiques to define tools and their parameters, the
-goal is that each tool can be interacted with as follows:
+Ultimately, through using Boutiques to define tools and their parameters,
+the goal is that each tool can be interacted with as follows:
 
 ```bash
 $ # Using Boutiques directly, the "exec launch" commands will run the app
@@ -28,6 +28,6 @@ $ bids-launch bids-app --input-dataset /path/to/bids /path/to/derivatives \
     --random-seed 0xBID5CAFE
 ```
 
-In the next sections, the `bids-app` tool, a Boutiques descriptor, and the
-`input_params.json`, a set of invocation parameters corresponding to this app,
+In the next sections, the `bids-app` tool, a Boutiques descriptor,
+and the `input_params.json`, a set of invocation parameters corresponding to this app,
 will be defined.