diff --git a/.github/workflows/js-ci.yml b/.github/workflows/js-ci.yml
index c35c2f2b0b4..c6e23434716 100644
--- a/.github/workflows/js-ci.yml
+++ b/.github/workflows/js-ci.yml
@@ -33,9 +33,6 @@ jobs:
           name: ${{ github.job }}
   lint-docs:
     runs-on: ubuntu-latest
-    defaults:
-      run:
-        working-directory: docs
     env:
       NODE_OPTIONS: --max-old-space-size=4096
     steps:
@@ -43,4 +40,4 @@ jobs:
       - uses: actions/setup-node@v4
         with:
           node-version-file: 'catalog/package.json'
-      - run: npx --package=markdownlint-cli markdownlint --ignore node_modules **/*.md
+      - run: npx --package=markdownlint-cli markdownlint .
diff --git a/.markdownlintignore b/.markdownlintignore
new file mode 100644
index 00000000000..b395cd061db
--- /dev/null
+++ b/.markdownlintignore
@@ -0,0 +1,12 @@
+# Not ready for lint yet
+gendocs
+lambdas
+py-shared
+testdocs
+
+# Autogenerated 
+docs/api-reference
+
+.git
+catalog/node_modules
+venv
diff --git a/catalog/CHANGELOG.md b/catalog/CHANGELOG.md
index 69103a025bb..657a4534516 100644
--- a/catalog/CHANGELOG.md
+++ b/catalog/CHANGELOG.md
@@ -16,5 +16,9 @@ where verb is one of
 
 ## Changes
 
-- [Added] Support `ui.actions.downloadObject` and `ui.actions.downloadPackage` options for configuring visibility of download buttons under "Bucket" and "Packages" respectively ([#4111](https://github.com/quiltdata/quilt/pull/4111))
-- [Added] Bootstrap the change log ([#4112](https://github.com/quiltdata/quilt/pull/4112))
+- [Added] Support `ui.actions.downloadObject` and `ui.actions.downloadPackage`
+options for configuring visibility of download buttons under "Bucket"
+and "Packages" respectively
+([#4111](https://github.com/quiltdata/quilt/pull/4111))
+- [Added] Bootstrap the change log
+([#4112](https://github.com/quiltdata/quilt/pull/4112))
diff --git a/catalog/README.md b/catalog/README.md
index 5c3f310704d..933afe6b259 100644
--- a/catalog/README.md
+++ b/catalog/README.md
@@ -2,8 +2,6 @@
 
 The catalog is a web frontend for browsing meta-data held by the Quilt registry.
 
-# Developer
-
 ## Configuration
 
 The app configuration (API endpoints, bucket federations, etc.) is read from
@@ -41,8 +39,10 @@ $ npm start
 
 ### Fetch
 
-- An accurate check for a successful fetch() would include checking that the promise resolved, then checking that the Response.ok property has a value of true. The code would look something like this:
-  [msdn fetch doc](https://developer.mozilla.org/en-US/docs/Web/API/Fetch_API/Using_Fetch)
+- An accurate check for a successful fetch() would include checking that
+the promise resolved, then checking that the Response.ok property has
+a value of true. The code would look something like this:
+ [msdn fetch doc](https://developer.mozilla.org/en-US/docs/Web/API/Fetch_API/Using_Fetch)
 
 ## Deployment (for Quilt internal usage)
 
diff --git a/docs/CHUNKED_CHECKSUMS.md b/docs/CHUNKED_CHECKSUMS.md
index 3238920fda3..31f7bcad3b0 100644
--- a/docs/CHUNKED_CHECKSUMS.md
+++ b/docs/CHUNKED_CHECKSUMS.md
@@ -25,16 +25,16 @@ The key differences are:
 
 It can reuse hashes generated by
 [create_multipart_upload](https://boto3.amazonaws.com/v1/documentation/api/latest/reference/services/s3/client/create_multipart_upload.html)
-as of at least [boto3 1.34.44](https://pypi.org/project/boto3/1.34.44/) 
+as of at least [boto3 1.34.44](https://pypi.org/project/boto3/1.34.44/)
 (2024-02-16), simply by rehashing the value if source_size < 8 MiB.
 
+<!-- markdownlint-disable line-length -->
 ## Multiformats Registration
 
 * Name: sha2-256-chunked
 * Prefix: 0xb510
 * Status: draft
 * Type: multihash
-* Description: Hash of concatenated SHA2-256 digests of 8*2^n MiB source chunks;
-  n = ceil(log2(source_size/(10^4 * 8MiB)))
-* Registrar: [multiformats/multicodec](https://github.com/multiformats/multicodec) 
-* Registration Date: [2024-02-23](https://github.com/multiformats/multicodec/pull/343)
\ No newline at end of file
+* Description: Hash of concatenated SHA2-256 digests of 8*2^n MiB source chunks; n = ceil(log2(source_size/(10^4*8MiB)))
+* Registrar: [multiformats/multicodec](https://github.com/multiformats/multicodec)
+* Registration Date: [2024-02-23](https://github.com/multiformats/multicodec/pull/343)
diff --git a/docs/advanced-features/sso-permissions.md b/docs/advanced-features/sso-permissions.md
index ced4706a477..b90d1994a62 100644
--- a/docs/advanced-features/sso-permissions.md
+++ b/docs/advanced-features/sso-permissions.md
@@ -1,3 +1,4 @@
+<!-- markdownlint-disable no-blanks-blockquote -->
 # SSO permissions mapping
 
 > This feature requires Quilt stack version 1.54.0 or higher