Refactor server architecture to separate concerns and enable stdio transport

.github/actions/setup-python-env/action.yml

@@ -104,6 +104,9 @@ runs:
       if: inputs.skip-mise-setup != 'true'
       shell: bash
       run: |
-        export PATH="$HOME/.local/bin:$PATH" -E ci
+        export PATH="$HOME/.local/bin:$PATH"
+        export MISE_ENV="ci"
+        export MISE_YES=1
         mise trust --all
-        mise run setup > /dev/null 2>&1 || true
+        # Guard heavy setup with a timeout to limit runner memory and time usage in CI
+        timeout 10m mise run setup > /dev/null 2>&1 || true

.github/workflows/claude.yml

@@ -35,7 +35,7 @@ jobs:
       VOYAGE_API_KEY: ${{ secrets.VOYAGE_API_KEY }}
       CODEWEAVER_PROJECT_PATH: ${{ github.workspace }}
       MISE_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-      MISE_ENV: "ci"
+      MISE_ENV: "cloudagent"
     steps:
       - name: Checkout Repository
         uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8
@@ -55,7 +55,7 @@ jobs:
           base_branch: main
           use_commit_signing: true
           claude_args: |
-            --max-turns 30
+            --max-turns 100
             --allowedTools Bash,Batch,Glob,Grep,ToDoWrite,View,mcp__context7__get-library-docs,mcp__context7__resolve-library-id,mcp__sequential-thinking__sequentialthinking,mcp__github_ci__get_workflow_run_details,mcp__codeweaver__find_code
             --mcp-config .mcp.json
           prompt: |
@@ -82,8 +82,8 @@ jobs:
           use_commit_signing: true
           base_branch: main
           claude_args: |
-            --max-turns 30
-            --allowedTools Bash,Batch,Glob,Grep,ToDoWrite,View,mcp__context7__get-library-docs,mcp__context7__resolve-library-id,mcp__sequential-thinking__sequentialthinking,mcp__github_ci__get_workflow_run_details,mcp__codeweaver__find_code
+            --max-turns 100
+            --allowedTools Bash,Batch,Glob,Grep,ToDoWrite,View,mcp__context7__get-library-docs,mcp__context7__resolve-library-id,mcp__sequential-thinking__sequentialthinking,mcp__github_ci__get_workflow_run_details,mcp__codeweaver__find_code,WebFetch,WebSearch
             --mcp-config .mcp.json
           prompt: |
             REPO: ${{ github.repository }}
@@ -108,7 +108,7 @@ jobs:
           use_commit_signing: true
           base_branch: main
           claude_args: |
-            --max-turns 30
+            --max-turns 50
             --allowedTools Bash,Batch,Glob,Grep,ToDoWrite,View,mcp__context7__get-library-docs,mcp__context7__resolve-library-id,mcp__sequential-thinking__sequentialthinking,mcp__github_ci__get_workflow_run_details,mcp__codeweaver__find_code
             --mcp-config .mcp.json
           prompt: |
@@ -136,8 +136,8 @@ jobs:
           use_commit_signing: true
           base_branch: main
           claude_args: |
-            --max-turns 30
-            --allowedTools Bash,Batch,Glob,Grep,ToDoWrite,View,mcp__context7__get-library-docs,mcp__context7__resolve-library-id,mcp__sequential-thinking__sequentialthinking,mcp__github_ci__get_workflow_run_details,mcp__codeweaver__find_code
+            --max-turns 200
+            --allowedTools Bash,Batch,Glob,Grep,ToDoWrite,View,mcp__context7__get-library-docs,mcp__context7__resolve-library-id,mcp__sequential-thinking__sequentialthinking,mcp__github_ci__get_workflow_run_details,mcp__codeweaver__find_code,WebFetch,WebSearch
             --mcp-config .mcp.json
           prompt: |
             REPO: ${{ github.repository }}

.github/workflows/copilot-setup-steps.yml

@@ -23,16 +23,16 @@ jobs:
       VOYAGE_API_KEY: ${{ secrets.VOYAGE_API_KEY }}
       CODEWEAVER_PROJECT_PATH: ${{ github.workspace }}
       MISE_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-      MISE_ENV: "ci"
+      MISE_ENV: "cloudagent"
       MISE_YES: 1
     runs-on: ubuntu-latest
+    # Add an overall job timeout so we don't let runaway installs exhaust the runner indefinitely
+    timeout-minutes: 50
     # Set the permissions to the lowest permissions possible needed for your steps.
     # Copilot will be given its own token for its operations.
     permissions:
-      # If you want to clone the repository as part of your setup steps, for example to install dependencies, you'll need the `contents: read` permission. If you don't clone the repository in your[...]
+      # If you want to clone the repository as part of your setup steps, for example to install dependencies, you'll need the `contents: read` permission.
       contents: write
-    # You can define any steps you want, and they will run before the agent starts.
-    # If you do not check out your code, Copilot will do this for you.
     steps:
       - name: Checkout code
         uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8
@@ -45,7 +45,7 @@ jobs:
             ~/.local/share/mise
             ~/.local/bin/mise
             ~/.local/share/mise/shims
-            ~/. cache/mise
+            ~/.cache/mise
             ~/.local/bin
           key: mise-copilot-${{ runner.os }}-${{ hashFiles('mise.ci.toml') }}
           restore-keys: |
@@ -60,7 +60,7 @@ jobs:
           key: uv-copilot-${{ runner.os }}-${{ hashFiles('uv.lock') }}
           restore-keys: |
             uv-copilot-${{ runner.os }}-
-            uv-${{ runner. os }}-
+            uv-${{ runner.os }}-
       - uses: jdx/mise-action@fcec31d82eb5c88cd7eb3fe3c270cb093aeeef18
         with:
           # Disable automatic env export to avoid hanging on enter hook in CI
@@ -76,15 +76,21 @@ jobs:
             cd codeweaver
           fi
           echo "Mise setup in directory: $(pwd)"
-          MISE="$(which mise)"
+          MISE="$(which mise || true)"
+          if [ -z "$MISE" ]; then
+            echo "mise not found on PATH; skipping install step"
+            exit 0
+          fi
           export MISE
           MISE_DIR="$(dirname "$MISE")"
           export MISE_DIR
           # Trust the config globally
           "$MISE" --quiet -y trust
           # Also set the trusted config paths environment variable for subprocesses
-          echo "MISE_TRUSTED_CONFIG_PATHS=$PWD/mise.toml:$PWD/mise.ci.toml" >> "$GITHUB_ENV"
-          "$MISE" --quiet -y install 2>&1 || echo "Warning: Some tools failed to install due to network limitations in CI environment"
+          echo "MISE_TRUSTED_CONFIG_PATHS=$PWD/mise.toml:$PWD/mise.cloudagent.toml" >> "$GITHUB_ENV"
+          # Guard the install with a timeout to prevent OOM / runaway installs in CI
+          # If the install fails or timeouts, we continue with a warning so Copilot can still run.
+          timeout 10m "$MISE" --quiet -y install 2>&1 || echo "Warning: Some tools failed to install due to network limitations or timeout in CI environment"
         env:
           MISE_DIR: ${{ runner.temp }}/mise
       - name: Configure Mise and Activate Environment

.github/workflows/docker.yml

@@ -34,7 +34,8 @@ on:
   workflow_dispatch:
     inputs:
       update_description_only:
-        description: 'Only update Docker Hub description (no build)'
+        description: "Only update Docker Hub description (no build)"
+        description: "Only update Docker Hub description (no build)"
         required: false
         type: boolean
         default: false
@@ -168,14 +169,15 @@ jobs:
             echo "Error: .git directory not found!"
             exit 1
           fi
+          # .github/workflows/docker.yml
       - name: Create test environment file
         run: |
           cat > .env << EOF
           PROJECT_PATH=.
           CODEWEAVER_PORT=9328
           QDRANT_PORT=6333
           QDRANT_GRPC_PORT=6334
-          VOYAGE_API_KEY=test-key-for-compose-test
+          CODEWEAVER_PROFILE=quickstart  # ← Add this
           COLLECTION_NAME=codeweaver-test
           ENABLE_TELEMETRY=false
           LOG_LEVEL=INFO
@@ -184,23 +186,29 @@ jobs:
         run: |
           docker compose build
           docker compose up -d
+          # .github/workflows/docker.yml
       - name: Wait for services to be healthy
         run: |
           echo "Waiting for Qdrant to be ready..."
           timeout 60 bash -c 'until curl -sf http://localhost:6333/health; do sleep 2; done'
 
           echo "Waiting for CodeWeaver to be ready..."
-          # CodeWeaver may take longer due to initial setup
-          timeout 120 bash -c 'until curl -sf http://localhost:9328/health/ 2>/dev/null; do sleep 5; done' || true
+          # Increase timeout to 5 minutes for initial model downloads
+          timeout 300 bash -c 'until curl -sf http://localhost:9328/health/ 2>/dev/null; do echo "Waiting for CodeWeaver (may download models on first run)..."; sleep 10; done'
       - name: Test Qdrant accessibility
+        env:
+          QDRANT_HEALTH_URL: http://localhost:6333/healthz
         run: |
           echo "Testing Qdrant health endpoint..."
-          curl -f http://localhost:6333/health || (docker compose logs qdrant && exit 1)
+          curl -sf "$QDRANT_HEALTH_URL" || (echo "Qdrant health check failed" && docker compose logs qdrant && exit 1)
+          echo "Qdrant health check passed!"
       - name: Test CodeWeaver accessibility
+        env:
+          CODEWEAVER_HEALTH_URL: http://localhost:9328/health/
         run: |
           echo "Testing CodeWeaver health endpoint..."
           curl -f http://localhost:9328/health/ || (docker compose logs codeweaver && exit 1)
-        continue-on-error: true # May fail without valid API key, but we test connectivity
+          curl -f http://localhost:9328/health/ || (docker compose logs codeweaver && exit 1)
       - name: Check logs for errors
         if: always()
         run: |