feat: codebase map, Azure reader, type-aware ingestion, SonarCloud security gate

.env.example

@@ -111,3 +111,34 @@ METADATA_EXTRACTION_MODE=keyword
 # METADATA_EXTRACTION_MODE=ollama).  Pull it first:
 #   ollama pull qwen3:0.6b
 OLLAMA_CLASSIFY_MODEL=qwen3:0.6b
+
+# ── Codebase map: Magika file-type detection ────────────────────────
+# Path to the Magika CLI binary. Install via `brew install magika`.
+# If not found, falls back to suffix-based detection.
+# MAGIKA_BINARY=magika
+
+# ── Codebase map: document similarity threshold ─────────────────────
+# Cosine similarity threshold for document graph edges (default 0.85).
+# Lower = more edges, higher = fewer edges. Needs calibration experiment.
+# DOC_SIMILARITY_THRESHOLD=0.85
+
+# ── Codebase map: cache directory ───────────────────────────────────
+# Per-project cache for codebase map, keyed by git commit hash.
+# CODEBASE_MAP_CACHE_DIR=.opencode
+
+# ── Codebase map: file count and depth limits ───────────────────────
+# Maximum number of files to scan before truncating (default 5000).
+# CODEBASE_MAP_MAX_FILES=5000
+# Maximum directory depth for recursive scanning (default 10).
+# CODEBASE_MAP_MAX_DEPTH=10
+
+# ── Document backend selection ──────────────────────────────────────
+# Controls document parsing backend. Accepted: "local" (default), "azure".
+# "local" uses LiteParse → pypdfium2 → pypdf chain.
+# "azure" uses Azure Document Intelligence with automatic fallback to local.
+DOCUMENT_BACKEND=local
+
+# Azure Document Intelligence credentials (only needed when DOCUMENT_BACKEND=azure).
+# AZURE_DOC_INTELLIGENCE_ENDPOINT=https://<resource>.cognitiveservices.azure.com/
+# AZURE_DOC_INTELLIGENCE_KEY=
+# AZURE_DOC_INTELLIGENCE_MODEL=prebuilt-layout

.github/workflows/ci.yml

@@ -13,10 +13,6 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest]
-        extra: ['', 'pdf-liteparse']
-        exclude:
-          - os: ubuntu-latest
-            extra: pdf-liteparse  # LiteParse native binary is macOS arm64 only for now
 
     steps:
       - uses: actions/checkout@v5
@@ -30,20 +26,43 @@ jobs:
         run: pip install uv
 
       - name: Install dependencies
-        run: |
-          if [ -n "${{ matrix.extra }}" ]; then
-            uv sync --extra ${{ matrix.extra }}
-          else
-            uv sync
-          fi
+        run: uv sync
 
       - name: Run tests (fast)
         env:
           PDF_READER: pypdf
         run: uv run pytest -m "not slow" --tb=short -q
 
-      - name: Run tests (slow, liteparse only)
-        if: matrix.extra == 'pdf-liteparse'
+      - name: Run tests (slow, liteparse on macOS)
+        if: matrix.os == 'macos-latest'
         env:
           PDF_READER: liteparse
         run: uv run pytest -m "slow" --tb=short -q || echo "Slow tests skipped (Ollama not available in CI)"
+
+  sonarcloud:
+    name: SonarCloud Scan
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v3
+
+      - name: Install dependencies
+        run: uv sync
+
+      - name: Run tests with coverage
+        run: uv run pytest -m "not slow" --cov=rag_mcp --cov-report=xml
+
+      - name: SonarCloud Scan
+        uses: SonarSource/sonarcloud-github-action@master
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}

.gitignore

@@ -49,9 +49,16 @@ coverage.xml
 *.swo
 *~
 
+# Codebase map cache (per-project, keyed by git commit)
+.opencode/codebase-graph.json
+.opencode/magika-inventory.json
+
 # Generated knowledge graph artifacts
 graphify-out/
 
 # OS
 .DS_Store
 Thumbs.db
+
+# Project Management
+/niftypm

.opencode/opencode.json

@@ -1,6 +1,19 @@
 {
   "$schema": "https://opencode.ai/config.json",
-  "plugin": [
-    ".opencode/plugins/graphify.js"
-  ]
-}
+  "plugin": [".opencode/plugins/graphify.js"],
+  "mcp": {
+    "sonarqube": {
+      "type": "local",
+      "command": [
+        "java",
+        "-jar",
+        "/Users/aizat/Development/PROJECTS/sonarqube-mcp-server/build/libs/sonarqube-mcp-server-1.22-SNAPSHOT.jar"
+      ],
+      "env": {
+        "STORAGE_PATH": "/Users/aizat/Development/PROJECTS/sonarqube-mcp-server/storage",
+        "SONARQUBE_TOKEN": "${SONARQUBE_CLI_TOKEN}",
+        "SONARQUBE_ORG": "${SONARQUBE_CLI_ORG}"
+      }
+    }
+  }
+}

.opencode/plugins/fast-context.ts

@@ -0,0 +1,43 @@
+/**
+ * Fast Context Codebase Map Plugin for OpenCode.
+ *
+ * Injects a compact codebase map into the agent's system prompt at the
+ * start of each session. The map is fetched once per session via the
+ * `get_codebase_map` MCP tool and cached for the session duration.
+ *
+ * Auto-discovered when placed in `.opencode/plugins/`.
+ */
+
+import type { Plugin } from "@opencode-ai/plugin";
+
+const injected = new Set<string>();
+
+export const FastContextPlugin: Plugin = async ({ directory, $ }) => {
+  return {
+    "experimental.chat.system.transform": async (input, output) => {
+      const sessionID = input.sessionID;
+      if (!sessionID || injected.has(sessionID)) {
+        return;
+      }
+
+      try {
+        const proc =
+          $`uv run python -c "from rag_mcp.codebase_map import get_codebase_map_text; print(get_codebase_map_text(path='.', refresh=False))"`
+            .cwd(directory)
+            .quiet()
+            .nothrow();
+        const result = await proc.text();
+
+        if (result && !result.includes('"status": "error"')) {
+          output.system.push(`# Codebase Map\n\n${result}`);
+          injected.add(sessionID);
+        }
+      } catch (err) {
+        // Silently fail — the map is a convenience, not a requirement.
+        console.error("[fast-context] Failed to fetch codebase map:", err);
+      }
+    },
+  };
+};
+
+export default FastContextPlugin;

.sonarlint/connectedMode.json

@@ -0,0 +1,5 @@
+{
+    "sonarCloudOrganization": "cmdaltctr",
+    "projectKey": "cmdaltctr_llamaindex-rag-mcp",
+    "region": "EU"
+}