K8:Refactors and configures indexer deployments

deploy/kubernetes/configmap.yaml

@@ -37,6 +37,9 @@ data:
   INDEX_CHUNK_OVERLAP: '10'
   INDEX_MICRO_CHUNKS: '0'
   INDEX_SEMANTIC_CHUNKS: '1'
+  INDEX_UPSERT_BACKOFF: '0.5'
+  INDEX_UPSERT_BATCH: '128'
+  INDEX_UPSERT_RETRIES: '5'
   LLAMACPP_EXTRA_ARGS: ''
   LLAMACPP_GPU_LAYERS: '32'
   LLAMACPP_GPU_SPLIT: ''
@@ -47,7 +50,7 @@ data:
   LLM_EXPAND_MAX: '0'
   LLM_EXPAND_MODEL: phi3:mini
   LLM_PROVIDER: ollama
-  MAX_CHANGED_SYMBOLS_RATIO: '0.6  # If >60% of symbols changed, do full reprocessing'
+  MAX_CHANGED_SYMBOLS_RATIO: '0.6'
   MAX_EMBED_CACHE: '16384'
   MAX_MICRO_CHUNKS_PER_FILE: '500'
   MCP_INDEXER_URL: http://localhost:8003/mcp
@@ -68,12 +71,13 @@ data:
   MULTI_REPO_MODE: '1'
   OLLAMA_HOST: http://host.docker.internal:11434
   PRF_ENABLED: '1'
+  QDRANT_API_KEY: ''
   QDRANT_TIMEOUT: '20'
   QDRANT_URL: http://qdrant:6333
   REFRAG_CANDIDATES: '200'
   REFRAG_COMMIT_DESCRIBE: '1'
   REFRAG_DECODER: '1'
-  REFRAG_DECODER_MODE: 'prompt  # prompt|soft'
+  REFRAG_DECODER_MODE: prompt
   REFRAG_ENCODER_MODEL: BAAI/bge-base-en-v1.5
   REFRAG_GATE_FIRST: '1'
   REFRAG_MODE: '1'

deploy/kubernetes/indexer-services.yaml

@@ -80,7 +80,6 @@ spec:
         volumeMounts:
         - name: work-volume
           mountPath: /work
-          readOnly: true
         - name: metadata-volume
           mountPath: /work/.codebase
         envFrom:
@@ -145,7 +144,6 @@ spec:
         volumeMounts:
         - name: work-volume
           mountPath: /work
-          readOnly: true
         - name: metadata-volume
           mountPath: /work/.codebase
         envFrom:
@@ -205,7 +203,6 @@ spec:
         volumeMounts:
         - name: work-volume
           mountPath: /work
-          readOnly: true
         - name: metadata-volume
           mountPath: /work/.codebase
         envFrom:

deploy/kubernetes/mcp-http.yaml

@@ -265,11 +265,6 @@ spec:
             configMapKeyRef:
               name: context-engine-config
               key: MEMORY_MCP_URL
-        - name: CTX_MULTI_COLLECTION
-          valueFrom:
-            configMapKeyRef:
-              name: context-engine-config
-              key: CTX_MULTI_COLLECTION
         - name: FASTMCP_HOST
           valueFrom:
             configMapKeyRef:

deploy/kubernetes/mcp-indexer.yaml

@@ -63,11 +63,6 @@ spec:
             configMapKeyRef:
               name: context-engine-config
               key: EMBEDDING_MODEL
-        - name: CTX_MULTI_COLLECTION
-          valueFrom:
-            configMapKeyRef:
-              name: context-engine-config
-              key: CTX_MULTI_COLLECTION
         resources:
           requests:
             memory: 512Mi

deploy/kubernetes/upload-service.yaml

@@ -104,7 +104,7 @@ spec:
       volumes:
       - name: work-volume
         persistentVolumeClaim:
-          claimName: upload-work-pvc
+          claimName: code-repos-pvc
       - name: codebase-volume
         persistentVolumeClaim:
           claimName: upload-codebase-pvc

scripts/sync_env_to_k8s.py

@@ -39,15 +39,52 @@ def parse_env_file(env_path: Path) -> dict:
     with env_path.open("r", encoding="utf-8") as f:
         for raw_line in f:
             line = raw_line.strip()
-            if not line or line.startswith("#"):
+            if not line:
                 continue
+
+            commented = False
+            if line.startswith("#"):
+                # Support commented defaults of the form "# KEY=VALUE" so that
+                # template-style .env files can still drive configmap.yaml.
+                stripped = line.lstrip("#").strip()
+                if "=" not in stripped:
+                    # Pure comment, skip.
+                    continue
+
+                key_part, value_part = stripped.split("=", 1)
+                key_candidate = key_part.strip()
+
+                # Only treat as a default if the key looks like an env var:
+                # UPPERCASE letters, digits, and underscores, with no spaces/colons.
+                if (
+                    not key_candidate
+                    or " " in key_candidate
+                    or ":" in key_candidate
+                    or not key_candidate.replace("_", "").isalnum()
+                    or not key_candidate.isupper()
+                ):
+                    # Looks like prose (e.g. "Repository mode: 0=...") rather than
+                    # an environment variable. Leave it as a comment.
+                    continue
+
+                line = f"{key_candidate}={value_part.strip()}"
+                commented = True
+
             if "=" not in line:
                 continue
             key, value = line.split("=", 1)
             key = key.strip()
             value = value.strip()
             if not key:
                 continue
+            # Do not let commented defaults override explicit KEY=VALUE entries
+            # that appeared earlier in the file.
+            if commented and key in data:
+                continue
+            # Strip inline shell-style comments from unquoted values, so that
+            # "VALUE  # comment" becomes just "VALUE".
+            if "#" in value and not (value.startswith("\"") or value.startswith("'")):
+                value = value.split("#", 1)[0].rstrip()
             # Strip single/double quotes if the whole value is quoted
             if (value.startswith("\"") and value.endswith("\"")) or (
                 value.startswith("'") and value.endswith("'")