Move .wdl MIME fix to Dockerfiles for reliability (PHP-130724)

The startup script approach was unreliable because post-startup.sh
could fail before reaching the MIME registration block. Move the fix
to Dockerfiles so it's baked into the container image at build time,
guaranteeing the MIME type is registered before RStudio Server starts.

Changes:
- Create Dockerfile for r-analysis with .wdl MIME type registration
- Update docker-compose.yaml to use build context
- Add MIME fix to r-analysis-aou Dockerfile
- Remove runtime MIME registration from post-startup.sh

Author: emmarogge

src/r-analysis-aou/Dockerfile

@@ -1,5 +1,10 @@
 FROM ghcr.io/rocker-org/devcontainer/tidyverse:4.5
 
+# Register .wdl (Workflow Description Language) as a text MIME type so RStudio
+# opens .wdl files as text instead of misidentifying them as binary (PHP-130724).
+COPY wdl.xml /usr/share/mime/packages/wdl.xml
+RUN update-mime-database /usr/share/mime
+
 ARG USER=rstudio
 ARG HOME=/home/$USER
 

src/r-analysis-aou/wdl.xml

@@ -0,0 +1,7 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<mime-info xmlns="http://www.freedesktop.org/standards/shared-mime-info">
+  <mime-type type="text/x-wdl">
+    <comment>Workflow Description Language</comment>
+    <glob pattern="*.wdl"/>
+  </mime-type>
+</mime-info>

src/r-analysis/Dockerfile

@@ -0,0 +1,6 @@
+FROM ghcr.io/rocker-org/devcontainer/tidyverse:4.5
+
+# Register .wdl (Workflow Description Language) as a text MIME type so RStudio
+# opens .wdl files as text instead of misidentifying them as binary (PHP-130724).
+COPY wdl.xml /usr/share/mime/packages/wdl.xml
+RUN update-mime-database /usr/share/mime

src/r-analysis/docker-compose.yaml

@@ -1,6 +1,8 @@
 services:
   app:
     container_name: "application-server"
+    build:
+      context: .
     image: "ghcr.io/rocker-org/devcontainer/tidyverse:4.5"
     restart: always
     volumes:

src/r-analysis/wdl.xml

@@ -0,0 +1,7 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<mime-info xmlns="http://www.freedesktop.org/standards/shared-mime-info">
+  <mime-type type="text/x-wdl">
+    <comment>Workflow Description Language</comment>
+    <glob pattern="*.wdl"/>
+  </mime-type>
+</mime-info>

startupscript/post-startup.sh

@@ -218,29 +218,6 @@ sed -i '/user_allow_other/s/^#//g' /etc/fuse.conf
 
 source "${CLOUD_SCRIPT_DIR}/resource-mount.sh"
 
-###############################
-# RStudio file type configuration
-###############################
-# Register additional file types as text to prevent RStudio from
-# misidentifying them as binary (PHP-130724).
-if command -v rstudio-server &> /dev/null; then
-  emit "Registering additional MIME types for RStudio..."
-  # Add WDL (Workflow Description Language) MIME type so RStudio
-  # recognizes .wdl files as text instead of binary.
-  cat > /usr/share/mime/packages/wdl.xml << 'MIME_EOF'
-<?xml version="1.0" encoding="UTF-8"?>
-<mime-info xmlns="http://www.freedesktop.org/standards/shared-mime-info">
-  <mime-type type="text/x-wdl">
-    <comment>Workflow Description Language</comment>
-    <glob pattern="*.wdl"/>
-  </mime-type>
-</mime-info>
-MIME_EOF
-  if command -v update-mime-database &> /dev/null; then
-    update-mime-database /usr/share/mime
-  fi
-fi
-
 ###############################
 # cloud platform specific setup
 ###############################