From 47dbf150973bd2540f61e3472c4a3a6933d4efed Mon Sep 17 00:00:00 2001
From: Alex Skrypnyk <alex@drevops.com>
Date: Thu, 1 Oct 2026 07:11:32 +1000
Subject: [PATCH 1/8] [#3169] Made 'nginx' depend on 'php' so Compose starts
 'php' before 'nginx' resolves its upstream.

---
 docker-compose.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/docker-compose.yml b/docker-compose.yml
index 78afa732a..e8099d703 100644
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -151,6 +151,7 @@ services:
     <<: [ *default-volumes, *default-user ]
     depends_on:
       - cli
+      - php
     networks:
       - default # This is a standard network and is used for all other environments, where requests routing is not required and/or not supported.
       - amazeeio-network ### This network is supported by Pygmy and used to route all requests to host machine locally. Removed in CI.

From 5efb93b8efaef7e5d95bbdea8f334a75afcc3e87 Mon Sep 17 00:00:00 2001
From: Alex Skrypnyk <alex@drevops.com>
Date: Thu, 1 Oct 2026 07:11:34 +1000
Subject: [PATCH 2/8] [#3169] Changed 'vortex-doctor' to recommend recreating
 the CLI container when the SSH key is missing inside it.

---
 .vortex/tooling/src/vortex-doctor      |   4 +-
 .vortex/tooling/tests/unit/doctor.bats | 131 +++++++++++++++++++++++++
 2 files changed, 133 insertions(+), 2 deletions(-)
 create mode 100644 .vortex/tooling/tests/unit/doctor.bats

diff --git a/.vortex/tooling/src/vortex-doctor b/.vortex/tooling/src/vortex-doctor
index e5b247c0e..1fa6a62c4 100755
--- a/.vortex/tooling/src/vortex-doctor
+++ b/.vortex/tooling/src/vortex-doctor
@@ -137,7 +137,7 @@ main() {
     # Check that the key is injected into pygmy ssh-agent container.
     if ! pygmy status 2>&1 | grep -q "${VORTEX_SSH_FILE}"; then
       warn "SSH key is not added to pygmy."
-      note "The SSH key will not be available in the CLI container. Run 'pygmy restart' and then 'ahoy up'."
+      note "The SSH key will not be available in the CLI container. Run 'pygmy restart' and then 'ahoy up --no-deps --force-recreate cli'."
     else
       ssh_key_added_to_pygmy=1
     fi
@@ -155,7 +155,7 @@ main() {
 
     if [ "${ssh_key_added_to_pygmy}" = "1" ] && [ "${ssh_key_volume_mounted}" = "1" ]; then
       if ! docker compose exec -T cli bash -c "ssh-add -l >/dev/null 2>&1"; then
-        fail "SSH key was not added to the container. Run 'pygmy restart'."
+        fail "SSH key was not added to the container. Run 'ahoy up --no-deps --force-recreate cli'."
       else
         pass "SSH key is available within the CLI container."
       fi
diff --git a/.vortex/tooling/tests/unit/doctor.bats b/.vortex/tooling/tests/unit/doctor.bats
new file mode 100644
index 000000000..7f816d635
--- /dev/null
+++ b/.vortex/tooling/tests/unit/doctor.bats
@@ -0,0 +1,131 @@
+#!/usr/bin/env bats
+##
+# Unit tests for the 'vortex-doctor' script.
+#
+# shellcheck disable=SC2030,SC2031,SC2034
+
+load ../_helper.bash
+
+# Runs the SSH check on its own: the helper disables every other host check
+# except the containers check.
+fixture_variables() {
+  export VORTEX_DOCTOR_CHECK_CONTAINERS=0
+  export VORTEX_DOCTOR_CHECK_SSH=1
+  export VORTEX_SSH_FILE="/home/user/.ssh/id_rsa"
+}
+
+@test "doctor: SSH key available in the CLI container passes the SSH check" {
+  pushd "${LOCAL_REPO_DIR}" >/dev/null || exit 1
+
+  fixture_variables
+
+  declare -a STEPS=(
+    "@pygmy status # 0 # [*] amazeeio-ssh-agent: Running as container amazeeio-ssh-agent\n4096 SHA256:fingerprint ${VORTEX_SSH_FILE} (RSA)"
+    '@docker compose exec -T cli bash -c grep "^/dev" /etc/mtab | grep -q /tmp/amazeeio_ssh-agent # 0'
+    "@docker compose exec -T cli bash -c ssh-add -l >/dev/null 2>&1 # 0"
+    "SSH key is available within the CLI container."
+    "- SSH key is not added to pygmy."
+    "- SSH key volume is not mounted into CLI container."
+    "- SSH key was not added to the container."
+    "All required checks have passed."
+  )
+  mocks="$(steps_run "setup")"
+
+  run .vortex/tooling/src/vortex-doctor
+  assert_success
+  steps_run "assert" "${mocks[@]}"
+
+  popd >/dev/null || exit 1
+}
+
+@test "doctor: unreachable SSH agent in the CLI container recommends recreating the CLI container" {
+  pushd "${LOCAL_REPO_DIR}" >/dev/null || exit 1
+
+  fixture_variables
+
+  declare -a STEPS=(
+    "@pygmy status # 0 # [*] amazeeio-ssh-agent: Running as container amazeeio-ssh-agent\n4096 SHA256:fingerprint ${VORTEX_SSH_FILE} (RSA)"
+    '@docker compose exec -T cli bash -c grep "^/dev" /etc/mtab | grep -q /tmp/amazeeio_ssh-agent # 0'
+    "@docker compose exec -T cli bash -c ssh-add -l >/dev/null 2>&1 # 2"
+    "SSH key was not added to the container. Run 'ahoy up --no-deps --force-recreate cli'."
+    "- Run 'pygmy restart'."
+    "- SSH key is available within the CLI container."
+    "- All required checks have passed."
+  )
+  mocks="$(steps_run "setup")"
+
+  run .vortex/tooling/src/vortex-doctor
+  assert_failure
+  steps_run "assert" "${mocks[@]}"
+
+  popd >/dev/null || exit 1
+}
+
+@test "doctor: SSH key missing from Pygmy recommends restarting Pygmy and recreating the CLI container" {
+  pushd "${LOCAL_REPO_DIR}" >/dev/null || exit 1
+
+  fixture_variables
+
+  declare -a STEPS=(
+    "@pygmy status # 0 # [*] amazeeio-ssh-agent: Running as container amazeeio-ssh-agent\nThe agent has no identities."
+    '@docker compose exec -T cli bash -c grep "^/dev" /etc/mtab | grep -q /tmp/amazeeio_ssh-agent # 0'
+    "SSH key is not added to pygmy."
+    "The SSH key will not be available in the CLI container. Run 'pygmy restart' and then 'ahoy up --no-deps --force-recreate cli'."
+    "- and then 'ahoy up'."
+    "- SSH key is available within the CLI container."
+    "- SSH key was not added to the container."
+    "All required checks have passed."
+  )
+  mocks="$(steps_run "setup")"
+
+  run .vortex/tooling/src/vortex-doctor
+  assert_success
+  steps_run "assert" "${mocks[@]}"
+
+  popd >/dev/null || exit 1
+}
+
+@test "doctor: SSH key volume missing from the CLI container recommends mounting it" {
+  pushd "${LOCAL_REPO_DIR}" >/dev/null || exit 1
+
+  fixture_variables
+
+  declare -a STEPS=(
+    "@pygmy status # 0 # [*] amazeeio-ssh-agent: Running as container amazeeio-ssh-agent\n4096 SHA256:fingerprint ${VORTEX_SSH_FILE} (RSA)"
+    '@docker compose exec -T cli bash -c grep "^/dev" /etc/mtab | grep -q /tmp/amazeeio_ssh-agent # 1'
+    "SSH key volume is not mounted into CLI container."
+    'Make sure that your "docker-compose.yml" has the following lines for CLI service:'
+    "volumes_from:"
+    "container:amazeeio-ssh-agent"
+    "After adding these lines, run 'ahoy up'."
+    "- SSH key is available within the CLI container."
+    "- SSH key was not added to the container."
+    "All required checks have passed."
+  )
+  mocks="$(steps_run "setup")"
+
+  run .vortex/tooling/src/vortex-doctor
+  assert_success
+  steps_run "assert" "${mocks[@]}"
+
+  popd >/dev/null || exit 1
+}
+
+@test "doctor: disabled SSH check skips the SSH key checks" {
+  pushd "${LOCAL_REPO_DIR}" >/dev/null || exit 1
+
+  fixture_variables
+  export VORTEX_DOCTOR_CHECK_SSH=0
+
+  mock_pygmy=$(mock_command "pygmy")
+  mock_docker=$(mock_command "docker")
+
+  run .vortex/tooling/src/vortex-doctor
+  assert_success
+  assert_output_contains "All required checks have passed."
+  assert_output_not_contains "SSH key"
+  assert_equal "0" "$(mock_get_call_num "${mock_pygmy}")"
+  assert_equal "0" "$(mock_get_call_num "${mock_docker}")"
+
+  popd >/dev/null || exit 1
+}

From 0300ea692046c44f1bf763f9148e4529e5bf62de Mon Sep 17 00:00:00 2001
From: Alex Skrypnyk <alex@drevops.com>
Date: Thu, 1 Oct 2026 07:11:35 +1000
Subject: [PATCH 3/8] [#3169] Documented recreating the CLI container after
 'pygmy restart' while the stack is running.

---
 .../content/development/environment/pygmy.mdx | 22 +++++++++++++++++++
 1 file changed, 22 insertions(+)

diff --git a/.vortex/docs/content/development/environment/pygmy.mdx b/.vortex/docs/content/development/environment/pygmy.mdx
index 05a3eab2c..c13442ecf 100644
--- a/.vortex/docs/content/development/environment/pygmy.mdx
+++ b/.vortex/docs/content/development/environment/pygmy.mdx
@@ -36,3 +36,25 @@ pygmy restart  # Restart the services.
 pygmy status   # Show the status of the services.
 pygmy clean    # Stop and remove all services. Useful if you have issues with pygmy.
 ```
+
+## SSH key in the CLI container
+
+The CLI container uses the SSH agent from Pygmy's `amazeeio-ssh-agent`
+container. It mounts the agent's volume through `volumes_from` and links to the
+agent's socket only when the CLI container starts.
+
+`pygmy restart` removes the agent container and creates a new one. If the stack
+is running at the time, the CLI container stays attached to the previous agent,
+so the SSH key is no longer available inside it. The same happens when the
+stack starts before Pygmy.
+
+Recreate the CLI container to attach it to the current agent:
+
+```shell
+ahoy up --no-deps --force-recreate cli
+```
+
+Running `ahoy up` on its own doesn't help: it leaves a running container as it
+is while its configuration stays the same. [`ahoy doctor`](doctor.mdx) checks
+that the SSH key is available in the CLI container and prints this command when
+it isn't.

From 1649bb4fcc7995c3ba8143796b0858f34206d0b3 Mon Sep 17 00:00:00 2001
From: Alex Skrypnyk <alex@drevops.com>
Date: Thu, 1 Oct 2026 07:12:31 +1000
Subject: [PATCH 4/8] [#3169] Updated Docker Compose config fixtures for the
 'nginx' dependency on 'php'.

---
 .vortex/tests/phpunit/Fixtures/docker-compose.env.json       | 4 ++++
 .vortex/tests/phpunit/Fixtures/docker-compose.env_local.json | 4 ++++
 .vortex/tests/phpunit/Fixtures/docker-compose.env_mod.json   | 4 ++++
 .vortex/tests/phpunit/Fixtures/docker-compose.noenv.json     | 4 ++++
 4 files changed, 16 insertions(+)

diff --git a/.vortex/tests/phpunit/Fixtures/docker-compose.env.json b/.vortex/tests/phpunit/Fixtures/docker-compose.env.json
index 4a8cfd3ca..c98d3aba7 100644
--- a/.vortex/tests/phpunit/Fixtures/docker-compose.env.json
+++ b/.vortex/tests/phpunit/Fixtures/docker-compose.env.json
@@ -341,6 +341,10 @@
                 "cli": {
                     "condition": "service_started",
                     "required": true
+                },
+                "php": {
+                    "condition": "service_started",
+                    "required": true
                 }
             },
             "entrypoint": null,
diff --git a/.vortex/tests/phpunit/Fixtures/docker-compose.env_local.json b/.vortex/tests/phpunit/Fixtures/docker-compose.env_local.json
index 4a8cfd3ca..c98d3aba7 100644
--- a/.vortex/tests/phpunit/Fixtures/docker-compose.env_local.json
+++ b/.vortex/tests/phpunit/Fixtures/docker-compose.env_local.json
@@ -341,6 +341,10 @@
                 "cli": {
                     "condition": "service_started",
                     "required": true
+                },
+                "php": {
+                    "condition": "service_started",
+                    "required": true
                 }
             },
             "entrypoint": null,
diff --git a/.vortex/tests/phpunit/Fixtures/docker-compose.env_mod.json b/.vortex/tests/phpunit/Fixtures/docker-compose.env_mod.json
index d976c8129..9c87a1d74 100644
--- a/.vortex/tests/phpunit/Fixtures/docker-compose.env_mod.json
+++ b/.vortex/tests/phpunit/Fixtures/docker-compose.env_mod.json
@@ -341,6 +341,10 @@
                 "cli": {
                     "condition": "service_started",
                     "required": true
+                },
+                "php": {
+                    "condition": "service_started",
+                    "required": true
                 }
             },
             "entrypoint": null,
diff --git a/.vortex/tests/phpunit/Fixtures/docker-compose.noenv.json b/.vortex/tests/phpunit/Fixtures/docker-compose.noenv.json
index 8e08ac611..8f9ad7295 100644
--- a/.vortex/tests/phpunit/Fixtures/docker-compose.noenv.json
+++ b/.vortex/tests/phpunit/Fixtures/docker-compose.noenv.json
@@ -341,6 +341,10 @@
                 "cli": {
                     "condition": "service_started",
                     "required": true
+                },
+                "php": {
+                    "condition": "service_started",
+                    "required": true
                 }
             },
             "entrypoint": null,

From 62507cbc61aa74550da9aee8e5c4cd1faf7029b7 Mon Sep 17 00:00:00 2001
From: Alex Skrypnyk <alex@drevops.com>
Date: Thu, 1 Oct 2026 07:12:38 +1000
Subject: [PATCH 5/8] Updated snapshots.

---
 .../handler_process/_baseline/docker-compose.yml   |  1 +
 .../docker-compose.yml                             |  6 +++---
 .../hosting_lagoon/docker-compose.yml              | 14 +++++++-------
 .../docker-compose.yml                             | 14 +++++++-------
 .../migration_disabled_lagoon/docker-compose.yml   | 14 +++++++-------
 .../migration_enabled/docker-compose.yml           |  4 ++--
 .../migration_enabled_circleci/docker-compose.yml  |  4 ++--
 .../migration_enabled_lagoon/docker-compose.yml    | 14 +++++++-------
 .../docker-compose.yml                             |  4 ++--
 .../docker-compose.yml                             |  4 ++--
 .../migration_fetch_source_ftp/docker-compose.yml  |  4 ++--
 .../docker-compose.yml                             |  4 ++--
 .../migration_fetch_source_s3/docker-compose.yml   |  4 ++--
 .../migration_fetch_source_url/docker-compose.yml  |  4 ++--
 .../non_interactive_config_file/docker-compose.yml |  4 ++--
 .../docker-compose.yml                             |  4 ++--
 .../provision_database_lagoon/docker-compose.yml   | 14 +++++++-------
 .../services_no_clamav/docker-compose.yml          |  4 ++--
 .../services_no_redis/docker-compose.yml           |  4 ++--
 .../services_no_solr/docker-compose.yml            |  6 +++---
 .../services_none/docker-compose.yml               |  6 +++---
 21 files changed, 69 insertions(+), 68 deletions(-)

diff --git a/.vortex/installer/tests/Fixtures/handler_process/_baseline/docker-compose.yml b/.vortex/installer/tests/Fixtures/handler_process/_baseline/docker-compose.yml
index 45c9d0b10..e3ec42b9f 100644
--- a/.vortex/installer/tests/Fixtures/handler_process/_baseline/docker-compose.yml
+++ b/.vortex/installer/tests/Fixtures/handler_process/_baseline/docker-compose.yml
@@ -121,6 +121,7 @@ services:
     <<: [ *default-volumes, *default-user ]
     depends_on:
       - cli
+      - php
     networks:
       - default # This is a standard network and is used for all other environments, where requests routing is not required and/or not supported.
       - amazeeio-network ### This network is supported by Pygmy and used to route all requests to host machine locally. Removed in CI.
diff --git a/.vortex/installer/tests/Fixtures/handler_process/custom_modules_search_without_solr/docker-compose.yml b/.vortex/installer/tests/Fixtures/handler_process/custom_modules_search_without_solr/docker-compose.yml
index 8c34eda32..104f70328 100644
--- a/.vortex/installer/tests/Fixtures/handler_process/custom_modules_search_without_solr/docker-compose.yml
+++ b/.vortex/installer/tests/Fixtures/handler_process/custom_modules_search_without_solr/docker-compose.yml
@@ -1,4 +1,4 @@
-@@ -155,17 +155,6 @@
+@@ -156,17 +156,6 @@
    redis:
      image: uselagoon/valkey-8:__VERSION__
  
@@ -16,7 +16,7 @@
    clamav:
      build:
        context: .
-@@ -196,13 +185,10 @@
+@@ -197,13 +186,10 @@
        - clamav
        - database
        - redis
@@ -30,7 +30,7 @@
  
  networks:           ### Use external networks locally. Automatically removed in CI.
    amazeeio-network: ### Automatically removed in CI.
-@@ -211,7 +197,6 @@
+@@ -212,7 +198,6 @@
  volumes:
    app: {}
    files: {}
diff --git a/.vortex/installer/tests/Fixtures/handler_process/hosting_lagoon/docker-compose.yml b/.vortex/installer/tests/Fixtures/handler_process/hosting_lagoon/docker-compose.yml
index 95a08119a..3460d1a23 100644
--- a/.vortex/installer/tests/Fixtures/handler_process/hosting_lagoon/docker-compose.yml
+++ b/.vortex/installer/tests/Fixtures/handler_process/hosting_lagoon/docker-compose.yml
@@ -17,7 +17,7 @@
  
    nginx:
      build:
-@@ -124,6 +129,11 @@
+@@ -125,6 +130,11 @@
      networks:
        - default # This is a standard network and is used for all other environments, where requests routing is not required and/or not supported.
        - amazeeio-network ### This network is supported by Pygmy and used to route all requests to host machine locally. Removed in CI.
@@ -29,7 +29,7 @@
  
    # PHP FPM container. All web requests are going through this container.
    php:
-@@ -139,6 +149,11 @@
+@@ -140,6 +150,11 @@
      <<: [ *default-volumes, *default-user ]
      depends_on:
        - cli
@@ -41,7 +41,7 @@
  
    database:
      build:
-@@ -151,9 +166,13 @@
+@@ -152,9 +167,13 @@
      <<: *default-user
      ports:
        - '3306' # Database port in a container. Find port on host with `ahoy info` or `docker compose port database 3306`.
@@ -55,7 +55,7 @@
  
    solr:
      build:
-@@ -165,6 +184,8 @@
+@@ -166,6 +185,8 @@
        - solr:/var/solr
      ports:
        - '8983' # Solr port in a container. Find port on host with `ahoy info` or `docker compose port solr 8983`.
@@ -64,7 +64,7 @@
  
    clamav:
      build:
-@@ -176,6 +197,10 @@
+@@ -177,6 +198,10 @@
        - '3310' # Find port on host with `docker compose port clamav 3310`.
      networks:
        - default
@@ -75,7 +75,7 @@
  
    # Chrome container, used for browser testing.
    chrome:
-@@ -188,6 +213,8 @@
+@@ -189,6 +214,8 @@
      ports:
        - '7900' # Find port on host with `docker compose port chrome 7900`.
      shm_size: '1gb' # Increase '/dev/shm' partition size to avoid browser crashing.
@@ -84,7 +84,7 @@
  
    # Helper container to wait for services to become available.
    wait-for-dependencies:
-@@ -203,6 +230,8 @@
+@@ -204,6 +231,8 @@
        - redis:6379
        - solr:8983
        - curl -s "http://solr:8983/solr/drupal/select?q=*:*&rows=0&wt=json" | grep response
diff --git a/.vortex/installer/tests/Fixtures/handler_process/hosting_project_name___lagoon/docker-compose.yml b/.vortex/installer/tests/Fixtures/handler_process/hosting_project_name___lagoon/docker-compose.yml
index 95a08119a..3460d1a23 100644
--- a/.vortex/installer/tests/Fixtures/handler_process/hosting_project_name___lagoon/docker-compose.yml
+++ b/.vortex/installer/tests/Fixtures/handler_process/hosting_project_name___lagoon/docker-compose.yml
@@ -17,7 +17,7 @@
  
    nginx:
      build:
-@@ -124,6 +129,11 @@
+@@ -125,6 +130,11 @@
      networks:
        - default # This is a standard network and is used for all other environments, where requests routing is not required and/or not supported.
        - amazeeio-network ### This network is supported by Pygmy and used to route all requests to host machine locally. Removed in CI.
@@ -29,7 +29,7 @@
  
    # PHP FPM container. All web requests are going through this container.
    php:
-@@ -139,6 +149,11 @@
+@@ -140,6 +150,11 @@
      <<: [ *default-volumes, *default-user ]
      depends_on:
        - cli
@@ -41,7 +41,7 @@
  
    database:
      build:
-@@ -151,9 +166,13 @@
+@@ -152,9 +167,13 @@
      <<: *default-user
      ports:
        - '3306' # Database port in a container. Find port on host with `ahoy info` or `docker compose port database 3306`.
@@ -55,7 +55,7 @@
  
    solr:
      build:
-@@ -165,6 +184,8 @@
+@@ -166,6 +185,8 @@
        - solr:/var/solr
      ports:
        - '8983' # Solr port in a container. Find port on host with `ahoy info` or `docker compose port solr 8983`.
@@ -64,7 +64,7 @@
  
    clamav:
      build:
-@@ -176,6 +197,10 @@
+@@ -177,6 +198,10 @@
        - '3310' # Find port on host with `docker compose port clamav 3310`.
      networks:
        - default
@@ -75,7 +75,7 @@
  
    # Chrome container, used for browser testing.
    chrome:
-@@ -188,6 +213,8 @@
+@@ -189,6 +214,8 @@
      ports:
        - '7900' # Find port on host with `docker compose port chrome 7900`.
      shm_size: '1gb' # Increase '/dev/shm' partition size to avoid browser crashing.
@@ -84,7 +84,7 @@
  
    # Helper container to wait for services to become available.
    wait-for-dependencies:
-@@ -203,6 +230,8 @@
+@@ -204,6 +231,8 @@
        - redis:6379
        - solr:8983
        - curl -s "http://solr:8983/solr/drupal/select?q=*:*&rows=0&wt=json" | grep response
diff --git a/.vortex/installer/tests/Fixtures/handler_process/migration_disabled_lagoon/docker-compose.yml b/.vortex/installer/tests/Fixtures/handler_process/migration_disabled_lagoon/docker-compose.yml
index 95a08119a..3460d1a23 100644
--- a/.vortex/installer/tests/Fixtures/handler_process/migration_disabled_lagoon/docker-compose.yml
+++ b/.vortex/installer/tests/Fixtures/handler_process/migration_disabled_lagoon/docker-compose.yml
@@ -17,7 +17,7 @@
  
    nginx:
      build:
-@@ -124,6 +129,11 @@
+@@ -125,6 +130,11 @@
      networks:
        - default # This is a standard network and is used for all other environments, where requests routing is not required and/or not supported.
        - amazeeio-network ### This network is supported by Pygmy and used to route all requests to host machine locally. Removed in CI.
@@ -29,7 +29,7 @@
  
    # PHP FPM container. All web requests are going through this container.
    php:
-@@ -139,6 +149,11 @@
+@@ -140,6 +150,11 @@
      <<: [ *default-volumes, *default-user ]
      depends_on:
        - cli
@@ -41,7 +41,7 @@
  
    database:
      build:
-@@ -151,9 +166,13 @@
+@@ -152,9 +167,13 @@
      <<: *default-user
      ports:
        - '3306' # Database port in a container. Find port on host with `ahoy info` or `docker compose port database 3306`.
@@ -55,7 +55,7 @@
  
    solr:
      build:
-@@ -165,6 +184,8 @@
+@@ -166,6 +185,8 @@
        - solr:/var/solr
      ports:
        - '8983' # Solr port in a container. Find port on host with `ahoy info` or `docker compose port solr 8983`.
@@ -64,7 +64,7 @@
  
    clamav:
      build:
-@@ -176,6 +197,10 @@
+@@ -177,6 +198,10 @@
        - '3310' # Find port on host with `docker compose port clamav 3310`.
      networks:
        - default
@@ -75,7 +75,7 @@
  
    # Chrome container, used for browser testing.
    chrome:
-@@ -188,6 +213,8 @@
+@@ -189,6 +214,8 @@
      ports:
        - '7900' # Find port on host with `docker compose port chrome 7900`.
      shm_size: '1gb' # Increase '/dev/shm' partition size to avoid browser crashing.
@@ -84,7 +84,7 @@
  
    # Helper container to wait for services to become available.
    wait-for-dependencies:
-@@ -203,6 +230,8 @@
+@@ -204,6 +231,8 @@
        - redis:6379
        - solr:8983
        - curl -s "http://solr:8983/solr/drupal/select?q=*:*&rows=0&wt=json" | grep response
diff --git a/.vortex/installer/tests/Fixtures/handler_process/migration_enabled/docker-compose.yml b/.vortex/installer/tests/Fixtures/handler_process/migration_enabled/docker-compose.yml
index ba9c983ea..c62947d38 100644
--- a/.vortex/installer/tests/Fixtures/handler_process/migration_enabled/docker-compose.yml
+++ b/.vortex/installer/tests/Fixtures/handler_process/migration_enabled/docker-compose.yml
@@ -15,7 +15,7 @@
  
  # The default user under which the containers should run.
  x-user: &default-user
-@@ -152,6 +162,19 @@
+@@ -153,6 +163,19 @@
      ports:
        - '3306' # Database port in a container. Find port on host with `ahoy info` or `docker compose port database 3306`.
  
@@ -35,7 +35,7 @@
    redis:
      image: uselagoon/valkey-8:__VERSION__
  
-@@ -195,11 +218,13 @@
+@@ -196,11 +219,13 @@
      depends_on:
        - clamav
        - database
diff --git a/.vortex/installer/tests/Fixtures/handler_process/migration_enabled_circleci/docker-compose.yml b/.vortex/installer/tests/Fixtures/handler_process/migration_enabled_circleci/docker-compose.yml
index ba9c983ea..c62947d38 100644
--- a/.vortex/installer/tests/Fixtures/handler_process/migration_enabled_circleci/docker-compose.yml
+++ b/.vortex/installer/tests/Fixtures/handler_process/migration_enabled_circleci/docker-compose.yml
@@ -15,7 +15,7 @@
  
  # The default user under which the containers should run.
  x-user: &default-user
-@@ -152,6 +162,19 @@
+@@ -153,6 +163,19 @@
      ports:
        - '3306' # Database port in a container. Find port on host with `ahoy info` or `docker compose port database 3306`.
  
@@ -35,7 +35,7 @@
    redis:
      image: uselagoon/valkey-8:__VERSION__
  
-@@ -195,11 +218,13 @@
+@@ -196,11 +219,13 @@
      depends_on:
        - clamav
        - database
diff --git a/.vortex/installer/tests/Fixtures/handler_process/migration_enabled_lagoon/docker-compose.yml b/.vortex/installer/tests/Fixtures/handler_process/migration_enabled_lagoon/docker-compose.yml
index 2e66f5314..3b18e9eca 100644
--- a/.vortex/installer/tests/Fixtures/handler_process/migration_enabled_lagoon/docker-compose.yml
+++ b/.vortex/installer/tests/Fixtures/handler_process/migration_enabled_lagoon/docker-compose.yml
@@ -34,7 +34,7 @@
  
    nginx:
      build:
-@@ -124,6 +139,11 @@
+@@ -125,6 +140,11 @@
      networks:
        - default # This is a standard network and is used for all other environments, where requests routing is not required and/or not supported.
        - amazeeio-network ### This network is supported by Pygmy and used to route all requests to host machine locally. Removed in CI.
@@ -46,7 +46,7 @@
  
    # PHP FPM container. All web requests are going through this container.
    php:
-@@ -139,6 +159,11 @@
+@@ -140,6 +160,11 @@
      <<: [ *default-volumes, *default-user ]
      depends_on:
        - cli
@@ -58,7 +58,7 @@
  
    database:
      build:
-@@ -151,9 +176,26 @@
+@@ -152,9 +177,26 @@
      <<: *default-user
      ports:
        - '3306' # Database port in a container. Find port on host with `ahoy info` or `docker compose port database 3306`.
@@ -85,7 +85,7 @@
  
    solr:
      build:
-@@ -165,6 +207,8 @@
+@@ -166,6 +208,8 @@
        - solr:/var/solr
      ports:
        - '8983' # Solr port in a container. Find port on host with `ahoy info` or `docker compose port solr 8983`.
@@ -94,7 +94,7 @@
  
    clamav:
      build:
-@@ -176,6 +220,10 @@
+@@ -177,6 +221,10 @@
        - '3310' # Find port on host with `docker compose port clamav 3310`.
      networks:
        - default
@@ -105,7 +105,7 @@
  
    # Chrome container, used for browser testing.
    chrome:
-@@ -188,6 +236,8 @@
+@@ -189,6 +237,8 @@
      ports:
        - '7900' # Find port on host with `docker compose port chrome 7900`.
      shm_size: '1gb' # Increase '/dev/shm' partition size to avoid browser crashing.
@@ -114,7 +114,7 @@
  
    # Helper container to wait for services to become available.
    wait-for-dependencies:
-@@ -195,14 +245,18 @@
+@@ -196,14 +246,18 @@
      depends_on:
        - clamav
        - database
diff --git a/.vortex/installer/tests/Fixtures/handler_process/migration_fetch_source_acquia/docker-compose.yml b/.vortex/installer/tests/Fixtures/handler_process/migration_fetch_source_acquia/docker-compose.yml
index ba9c983ea..c62947d38 100644
--- a/.vortex/installer/tests/Fixtures/handler_process/migration_fetch_source_acquia/docker-compose.yml
+++ b/.vortex/installer/tests/Fixtures/handler_process/migration_fetch_source_acquia/docker-compose.yml
@@ -15,7 +15,7 @@
  
  # The default user under which the containers should run.
  x-user: &default-user
-@@ -152,6 +162,19 @@
+@@ -153,6 +163,19 @@
      ports:
        - '3306' # Database port in a container. Find port on host with `ahoy info` or `docker compose port database 3306`.
  
@@ -35,7 +35,7 @@
    redis:
      image: uselagoon/valkey-8:__VERSION__
  
-@@ -195,11 +218,13 @@
+@@ -196,11 +219,13 @@
      depends_on:
        - clamav
        - database
diff --git a/.vortex/installer/tests/Fixtures/handler_process/migration_fetch_source_container_registry/docker-compose.yml b/.vortex/installer/tests/Fixtures/handler_process/migration_fetch_source_container_registry/docker-compose.yml
index ba9c983ea..c62947d38 100644
--- a/.vortex/installer/tests/Fixtures/handler_process/migration_fetch_source_container_registry/docker-compose.yml
+++ b/.vortex/installer/tests/Fixtures/handler_process/migration_fetch_source_container_registry/docker-compose.yml
@@ -15,7 +15,7 @@
  
  # The default user under which the containers should run.
  x-user: &default-user
-@@ -152,6 +162,19 @@
+@@ -153,6 +163,19 @@
      ports:
        - '3306' # Database port in a container. Find port on host with `ahoy info` or `docker compose port database 3306`.
  
@@ -35,7 +35,7 @@
    redis:
      image: uselagoon/valkey-8:__VERSION__
  
-@@ -195,11 +218,13 @@
+@@ -196,11 +219,13 @@
      depends_on:
        - clamav
        - database
diff --git a/.vortex/installer/tests/Fixtures/handler_process/migration_fetch_source_ftp/docker-compose.yml b/.vortex/installer/tests/Fixtures/handler_process/migration_fetch_source_ftp/docker-compose.yml
index ba9c983ea..c62947d38 100644
--- a/.vortex/installer/tests/Fixtures/handler_process/migration_fetch_source_ftp/docker-compose.yml
+++ b/.vortex/installer/tests/Fixtures/handler_process/migration_fetch_source_ftp/docker-compose.yml
@@ -15,7 +15,7 @@
  
  # The default user under which the containers should run.
  x-user: &default-user
-@@ -152,6 +162,19 @@
+@@ -153,6 +163,19 @@
      ports:
        - '3306' # Database port in a container. Find port on host with `ahoy info` or `docker compose port database 3306`.
  
@@ -35,7 +35,7 @@
    redis:
      image: uselagoon/valkey-8:__VERSION__
  
-@@ -195,11 +218,13 @@
+@@ -196,11 +219,13 @@
      depends_on:
        - clamav
        - database
diff --git a/.vortex/installer/tests/Fixtures/handler_process/migration_fetch_source_lagoon/docker-compose.yml b/.vortex/installer/tests/Fixtures/handler_process/migration_fetch_source_lagoon/docker-compose.yml
index ba9c983ea..c62947d38 100644
--- a/.vortex/installer/tests/Fixtures/handler_process/migration_fetch_source_lagoon/docker-compose.yml
+++ b/.vortex/installer/tests/Fixtures/handler_process/migration_fetch_source_lagoon/docker-compose.yml
@@ -15,7 +15,7 @@
  
  # The default user under which the containers should run.
  x-user: &default-user
-@@ -152,6 +162,19 @@
+@@ -153,6 +163,19 @@
      ports:
        - '3306' # Database port in a container. Find port on host with `ahoy info` or `docker compose port database 3306`.
  
@@ -35,7 +35,7 @@
    redis:
      image: uselagoon/valkey-8:__VERSION__
  
-@@ -195,11 +218,13 @@
+@@ -196,11 +219,13 @@
      depends_on:
        - clamav
        - database
diff --git a/.vortex/installer/tests/Fixtures/handler_process/migration_fetch_source_s3/docker-compose.yml b/.vortex/installer/tests/Fixtures/handler_process/migration_fetch_source_s3/docker-compose.yml
index ba9c983ea..c62947d38 100644
--- a/.vortex/installer/tests/Fixtures/handler_process/migration_fetch_source_s3/docker-compose.yml
+++ b/.vortex/installer/tests/Fixtures/handler_process/migration_fetch_source_s3/docker-compose.yml
@@ -15,7 +15,7 @@
  
  # The default user under which the containers should run.
  x-user: &default-user
-@@ -152,6 +162,19 @@
+@@ -153,6 +163,19 @@
      ports:
        - '3306' # Database port in a container. Find port on host with `ahoy info` or `docker compose port database 3306`.
  
@@ -35,7 +35,7 @@
    redis:
      image: uselagoon/valkey-8:__VERSION__
  
-@@ -195,11 +218,13 @@
+@@ -196,11 +219,13 @@
      depends_on:
        - clamav
        - database
diff --git a/.vortex/installer/tests/Fixtures/handler_process/migration_fetch_source_url/docker-compose.yml b/.vortex/installer/tests/Fixtures/handler_process/migration_fetch_source_url/docker-compose.yml
index ba9c983ea..c62947d38 100644
--- a/.vortex/installer/tests/Fixtures/handler_process/migration_fetch_source_url/docker-compose.yml
+++ b/.vortex/installer/tests/Fixtures/handler_process/migration_fetch_source_url/docker-compose.yml
@@ -15,7 +15,7 @@
  
  # The default user under which the containers should run.
  x-user: &default-user
-@@ -152,6 +162,19 @@
+@@ -153,6 +163,19 @@
      ports:
        - '3306' # Database port in a container. Find port on host with `ahoy info` or `docker compose port database 3306`.
  
@@ -35,7 +35,7 @@
    redis:
      image: uselagoon/valkey-8:__VERSION__
  
-@@ -195,11 +218,13 @@
+@@ -196,11 +219,13 @@
      depends_on:
        - clamav
        - database
diff --git a/.vortex/installer/tests/Fixtures/handler_process/non_interactive_config_file/docker-compose.yml b/.vortex/installer/tests/Fixtures/handler_process/non_interactive_config_file/docker-compose.yml
index 6fa4c05b2..692212f1d 100644
--- a/.vortex/installer/tests/Fixtures/handler_process/non_interactive_config_file/docker-compose.yml
+++ b/.vortex/installer/tests/Fixtures/handler_process/non_interactive_config_file/docker-compose.yml
@@ -7,7 +7,7 @@
  
  # The default user under which the containers should run.
  x-user: &default-user
-@@ -152,9 +150,6 @@
+@@ -153,9 +151,6 @@
      ports:
        - '3306' # Database port in a container. Find port on host with `ahoy info` or `docker compose port database 3306`.
  
@@ -17,7 +17,7 @@
    solr:
      build:
        context: .
-@@ -195,12 +190,10 @@
+@@ -196,12 +191,10 @@
      depends_on:
        - clamav
        - database
diff --git a/.vortex/installer/tests/Fixtures/handler_process/non_interactive_config_string/docker-compose.yml b/.vortex/installer/tests/Fixtures/handler_process/non_interactive_config_string/docker-compose.yml
index a98532e58..041b1b533 100644
--- a/.vortex/installer/tests/Fixtures/handler_process/non_interactive_config_string/docker-compose.yml
+++ b/.vortex/installer/tests/Fixtures/handler_process/non_interactive_config_string/docker-compose.yml
@@ -1,4 +1,4 @@
-@@ -166,17 +166,6 @@
+@@ -167,17 +167,6 @@
      ports:
        - '8983' # Solr port in a container. Find port on host with `ahoy info` or `docker compose port solr 8983`.
  
@@ -16,7 +16,7 @@
    # Chrome container, used for browser testing.
    chrome:
      image: selenium/standalone-chromium:__VERSION__
-@@ -193,12 +182,10 @@
+@@ -194,12 +183,10 @@
    wait-for-dependencies:
      image: drevops/docker-wait-for-dependencies:__VERSION__
      depends_on:
diff --git a/.vortex/installer/tests/Fixtures/handler_process/provision_database_lagoon/docker-compose.yml b/.vortex/installer/tests/Fixtures/handler_process/provision_database_lagoon/docker-compose.yml
index 95a08119a..3460d1a23 100644
--- a/.vortex/installer/tests/Fixtures/handler_process/provision_database_lagoon/docker-compose.yml
+++ b/.vortex/installer/tests/Fixtures/handler_process/provision_database_lagoon/docker-compose.yml
@@ -17,7 +17,7 @@
  
    nginx:
      build:
-@@ -124,6 +129,11 @@
+@@ -125,6 +130,11 @@
      networks:
        - default # This is a standard network and is used for all other environments, where requests routing is not required and/or not supported.
        - amazeeio-network ### This network is supported by Pygmy and used to route all requests to host machine locally. Removed in CI.
@@ -29,7 +29,7 @@
  
    # PHP FPM container. All web requests are going through this container.
    php:
-@@ -139,6 +149,11 @@
+@@ -140,6 +150,11 @@
      <<: [ *default-volumes, *default-user ]
      depends_on:
        - cli
@@ -41,7 +41,7 @@
  
    database:
      build:
-@@ -151,9 +166,13 @@
+@@ -152,9 +167,13 @@
      <<: *default-user
      ports:
        - '3306' # Database port in a container. Find port on host with `ahoy info` or `docker compose port database 3306`.
@@ -55,7 +55,7 @@
  
    solr:
      build:
-@@ -165,6 +184,8 @@
+@@ -166,6 +185,8 @@
        - solr:/var/solr
      ports:
        - '8983' # Solr port in a container. Find port on host with `ahoy info` or `docker compose port solr 8983`.
@@ -64,7 +64,7 @@
  
    clamav:
      build:
-@@ -176,6 +197,10 @@
+@@ -177,6 +198,10 @@
        - '3310' # Find port on host with `docker compose port clamav 3310`.
      networks:
        - default
@@ -75,7 +75,7 @@
  
    # Chrome container, used for browser testing.
    chrome:
-@@ -188,6 +213,8 @@
+@@ -189,6 +214,8 @@
      ports:
        - '7900' # Find port on host with `docker compose port chrome 7900`.
      shm_size: '1gb' # Increase '/dev/shm' partition size to avoid browser crashing.
@@ -84,7 +84,7 @@
  
    # Helper container to wait for services to become available.
    wait-for-dependencies:
-@@ -203,6 +230,8 @@
+@@ -204,6 +231,8 @@
        - redis:6379
        - solr:8983
        - curl -s "http://solr:8983/solr/drupal/select?q=*:*&rows=0&wt=json" | grep response
diff --git a/.vortex/installer/tests/Fixtures/handler_process/services_no_clamav/docker-compose.yml b/.vortex/installer/tests/Fixtures/handler_process/services_no_clamav/docker-compose.yml
index a98532e58..041b1b533 100644
--- a/.vortex/installer/tests/Fixtures/handler_process/services_no_clamav/docker-compose.yml
+++ b/.vortex/installer/tests/Fixtures/handler_process/services_no_clamav/docker-compose.yml
@@ -1,4 +1,4 @@
-@@ -166,17 +166,6 @@
+@@ -167,17 +167,6 @@
      ports:
        - '8983' # Solr port in a container. Find port on host with `ahoy info` or `docker compose port solr 8983`.
  
@@ -16,7 +16,7 @@
    # Chrome container, used for browser testing.
    chrome:
      image: selenium/standalone-chromium:__VERSION__
-@@ -193,12 +182,10 @@
+@@ -194,12 +183,10 @@
    wait-for-dependencies:
      image: drevops/docker-wait-for-dependencies:__VERSION__
      depends_on:
diff --git a/.vortex/installer/tests/Fixtures/handler_process/services_no_redis/docker-compose.yml b/.vortex/installer/tests/Fixtures/handler_process/services_no_redis/docker-compose.yml
index 6fa4c05b2..692212f1d 100644
--- a/.vortex/installer/tests/Fixtures/handler_process/services_no_redis/docker-compose.yml
+++ b/.vortex/installer/tests/Fixtures/handler_process/services_no_redis/docker-compose.yml
@@ -7,7 +7,7 @@
  
  # The default user under which the containers should run.
  x-user: &default-user
-@@ -152,9 +150,6 @@
+@@ -153,9 +151,6 @@
      ports:
        - '3306' # Database port in a container. Find port on host with `ahoy info` or `docker compose port database 3306`.
  
@@ -17,7 +17,7 @@
    solr:
      build:
        context: .
-@@ -195,12 +190,10 @@
+@@ -196,12 +191,10 @@
      depends_on:
        - clamav
        - database
diff --git a/.vortex/installer/tests/Fixtures/handler_process/services_no_solr/docker-compose.yml b/.vortex/installer/tests/Fixtures/handler_process/services_no_solr/docker-compose.yml
index 8c34eda32..104f70328 100644
--- a/.vortex/installer/tests/Fixtures/handler_process/services_no_solr/docker-compose.yml
+++ b/.vortex/installer/tests/Fixtures/handler_process/services_no_solr/docker-compose.yml
@@ -1,4 +1,4 @@
-@@ -155,17 +155,6 @@
+@@ -156,17 +156,6 @@
    redis:
      image: uselagoon/valkey-8:__VERSION__
  
@@ -16,7 +16,7 @@
    clamav:
      build:
        context: .
-@@ -196,13 +185,10 @@
+@@ -197,13 +186,10 @@
        - clamav
        - database
        - redis
@@ -30,7 +30,7 @@
  
  networks:           ### Use external networks locally. Automatically removed in CI.
    amazeeio-network: ### Automatically removed in CI.
-@@ -211,7 +197,6 @@
+@@ -212,7 +198,6 @@
  volumes:
    app: {}
    files: {}
diff --git a/.vortex/installer/tests/Fixtures/handler_process/services_none/docker-compose.yml b/.vortex/installer/tests/Fixtures/handler_process/services_none/docker-compose.yml
index f5ed51407..cad54237c 100644
--- a/.vortex/installer/tests/Fixtures/handler_process/services_none/docker-compose.yml
+++ b/.vortex/installer/tests/Fixtures/handler_process/services_none/docker-compose.yml
@@ -7,7 +7,7 @@
  
  # The default user under which the containers should run.
  x-user: &default-user
-@@ -152,31 +150,6 @@
+@@ -153,31 +151,6 @@
      ports:
        - '3306' # Database port in a container. Find port on host with `ahoy info` or `docker compose port database 3306`.
  
@@ -39,7 +39,7 @@
    # Chrome container, used for browser testing.
    chrome:
      image: selenium/standalone-chromium:__VERSION__
-@@ -193,16 +166,9 @@
+@@ -194,16 +167,9 @@
    wait-for-dependencies:
      image: drevops/docker-wait-for-dependencies:__VERSION__
      depends_on:
@@ -56,7 +56,7 @@
  
  networks:           ### Use external networks locally. Automatically removed in CI.
    amazeeio-network: ### Automatically removed in CI.
-@@ -211,7 +177,6 @@
+@@ -212,7 +178,6 @@
  volumes:
    app: {}
    files: {}

From e2939b7ff1fbdd54a9aea27f16f726ac3533707e Mon Sep 17 00:00:00 2001
From: Alex Skrypnyk <alex@drevops.com>
Date: Thu, 1 Oct 2026 07:18:42 +1000
Subject: [PATCH 6/8] [#3169] Reworded the Pygmy SSH key section to pass the
 'Vortex.Contractions' prose rule.

---
 .vortex/docs/content/development/environment/pygmy.mdx | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.vortex/docs/content/development/environment/pygmy.mdx b/.vortex/docs/content/development/environment/pygmy.mdx
index c13442ecf..a667469d6 100644
--- a/.vortex/docs/content/development/environment/pygmy.mdx
+++ b/.vortex/docs/content/development/environment/pygmy.mdx
@@ -54,7 +54,7 @@ Recreate the CLI container to attach it to the current agent:
 ahoy up --no-deps --force-recreate cli
 ```
 
-Running `ahoy up` on its own doesn't help: it leaves a running container as it
-is while its configuration stays the same. [`ahoy doctor`](doctor.mdx) checks
-that the SSH key is available in the CLI container and prints this command when
-it isn't.
+Running `ahoy up` on its own isn't enough: Docker Compose leaves a running
+container alone when its configuration hasn't changed. [`ahoy doctor`](doctor.mdx)
+checks that the SSH key is available in the CLI container and prints this
+command when it isn't.

From e1cff1889b9d796af79f0c80aff05181cc905e92 Mon Sep 17 00:00:00 2001
From: Alex Skrypnyk <alex@drevops.com>
Date: Thu, 1 Oct 2026 07:54:02 +1000
Subject: [PATCH 7/8] [#3169] Reset the 'MINIMAL' and 'PREFLIGHT' doctor
 presets in 'doctor.bats' so an inherited preset can't turn off the SSH check.

---
 .vortex/tooling/tests/unit/doctor.bats | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/.vortex/tooling/tests/unit/doctor.bats b/.vortex/tooling/tests/unit/doctor.bats
index 7f816d635..1caff7f9d 100644
--- a/.vortex/tooling/tests/unit/doctor.bats
+++ b/.vortex/tooling/tests/unit/doctor.bats
@@ -7,8 +7,11 @@
 load ../_helper.bash
 
 # Runs the SSH check on its own: the helper disables every other host check
-# except the containers check.
+# except the containers check. The MINIMAL and PREFLIGHT presets override the
+# per-check flags, so a preset inherited from the environment is reset.
 fixture_variables() {
+  export VORTEX_DOCTOR_CHECK_MINIMAL=0
+  export VORTEX_DOCTOR_CHECK_PREFLIGHT=0
   export VORTEX_DOCTOR_CHECK_CONTAINERS=0
   export VORTEX_DOCTOR_CHECK_SSH=1
   export VORTEX_SSH_FILE="/home/user/.ssh/id_rsa"

From dd1d0ecc2b4130da5241cfeb6aff83a0c47d4c60 Mon Sep 17 00:00:00 2001
From: Alex Skrypnyk <alex@drevops.com>
Date: Thu, 1 Oct 2026 07:56:52 +1000
Subject: [PATCH 8/8] [#3169] Reset only the 'MINIMAL' doctor preset in
 'doctor.bats', since 'PREFLIGHT' only defaults flags the fixture already
 sets.

---
 .vortex/tooling/tests/unit/doctor.bats | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/.vortex/tooling/tests/unit/doctor.bats b/.vortex/tooling/tests/unit/doctor.bats
index 1caff7f9d..4a792dc75 100644
--- a/.vortex/tooling/tests/unit/doctor.bats
+++ b/.vortex/tooling/tests/unit/doctor.bats
@@ -7,11 +7,10 @@
 load ../_helper.bash
 
 # Runs the SSH check on its own: the helper disables every other host check
-# except the containers check. The MINIMAL and PREFLIGHT presets override the
-# per-check flags, so a preset inherited from the environment is reset.
+# except the containers check. The MINIMAL preset overwrites the per-check
+# flags, so a preset inherited from the environment is reset.
 fixture_variables() {
   export VORTEX_DOCTOR_CHECK_MINIMAL=0
-  export VORTEX_DOCTOR_CHECK_PREFLIGHT=0
   export VORTEX_DOCTOR_CHECK_CONTAINERS=0
   export VORTEX_DOCTOR_CHECK_SSH=1
   export VORTEX_SSH_FILE="/home/user/.ssh/id_rsa"