Use single func to handle indexing from scratch and incrementally

Previous regenerate mechanism did not deduplicate entries with same key
So entries looked different between regenerate and update
Having single func, mark_entries_for_update, to handle both scenarios
will avoid this divergence

Update all text_to_jsonl methods to use the above method for
generating index from scratch

src/khoj/processor/github/github_to_jsonl.py

@@ -15,7 +15,6 @@ from khoj.processor.org_mode.org_to_jsonl import OrgToJsonl
 from khoj.processor.text_to_jsonl import TextToJsonl
 from khoj.utils.jsonl import dump_jsonl, compress_jsonl_data
 from khoj.utils.rawconfig import Entry
-from khoj.utils import state
 
 
 logger = logging.getLogger(__name__)
@@ -38,7 +37,7 @@ class GithubToJsonl(TextToJsonl):
         else:
             return
 
-    def process(self, previous_entries=None):
+    def process(self, previous_entries=[]):
         current_entries = []
         for repo in self.config.repos:
             current_entries += self.process_repo(repo)

src/khoj/processor/jsonl/jsonl_to_jsonl.py

@@ -16,7 +16,7 @@ logger = logging.getLogger(__name__)
 
 class JsonlToJsonl(TextToJsonl):
     # Define Functions
-    def process(self, previous_entries=None):
+    def process(self, previous_entries=[]):
         # Extract required fields from config
         input_jsonl_files, input_jsonl_filter, output_file = (
             self.config.input_files,
@@ -38,14 +38,8 @@ class JsonlToJsonl(TextToJsonl):
 
         # Identify, mark and merge any new entries with previous entries
         with timer("Identify new or updated entries", logger):
-            if not previous_entries:
-                entries_with_ids = list(enumerate(current_entries))
-            else:
             entries_with_ids = TextToJsonl.mark_entries_for_update(
-                    current_entries,
-                    previous_entries,
-                    key="compiled",
-                    logger=logger,
+                current_entries, previous_entries, key="compiled", logger=logger
             )
 
         with timer("Write entries to JSONL file", logger):

src/khoj/processor/markdown/markdown_to_jsonl.py

@@ -23,7 +23,7 @@ class MarkdownToJsonl(TextToJsonl):
         self.config = config
 
     # Define Functions
-    def process(self, previous_entries=None):
+    def process(self, previous_entries=[]):
         # Extract required fields from config
         markdown_files, markdown_file_filter, output_file = (
             self.config.input_files,
@@ -51,9 +51,6 @@ class MarkdownToJsonl(TextToJsonl):
 
         # Identify, mark and merge any new entries with previous entries
         with timer("Identify new or updated entries", logger):
-            if not previous_entries:
-                entries_with_ids = list(enumerate(current_entries))
-            else:
             entries_with_ids = TextToJsonl.mark_entries_for_update(
                 current_entries, previous_entries, key="compiled", logger=logger
             )

src/khoj/processor/notion/notion_to_jsonl.py

@@ -80,7 +80,7 @@ class NotionToJsonl(TextToJsonl):
 
         self.body_params = {"page_size": 100}
 
-    def process(self, previous_entries=None):
+    def process(self, previous_entries=[]):
         current_entries = []
 
         # Get all pages
@@ -240,9 +240,6 @@ class NotionToJsonl(TextToJsonl):
     def update_entries_with_ids(self, current_entries, previous_entries):
         # Identify, mark and merge any new entries with previous entries
         with timer("Identify new or updated entries", logger):
-            if not previous_entries:
-                entries_with_ids = list(enumerate(current_entries))
-            else:
             entries_with_ids = TextToJsonl.mark_entries_for_update(
                 current_entries, previous_entries, key="compiled", logger=logger
             )

src/khoj/processor/org_mode/org_to_jsonl.py

@@ -22,7 +22,7 @@ class OrgToJsonl(TextToJsonl):
         self.config = config
 
     # Define Functions
-    def process(self, previous_entries: List[Entry] = None):
+    def process(self, previous_entries: List[Entry] = []):
         # Extract required fields from config
         org_files, org_file_filter, output_file = (
             self.config.input_files,
@@ -51,9 +51,7 @@ class OrgToJsonl(TextToJsonl):
             current_entries = self.split_entries_by_max_tokens(current_entries, max_tokens=256)
 
         # Identify, mark and merge any new entries with previous entries
-        if not previous_entries:
-            entries_with_ids = list(enumerate(current_entries))
-        else:
+        with timer("Identify new or updated entries", logger):
             entries_with_ids = TextToJsonl.mark_entries_for_update(
                 current_entries, previous_entries, key="compiled", logger=logger
             )

src/khoj/processor/pdf/pdf_to_jsonl.py

@@ -19,7 +19,7 @@ logger = logging.getLogger(__name__)
 
 class PdfToJsonl(TextToJsonl):
     # Define Functions
-    def process(self, previous_entries=None):
+    def process(self, previous_entries=[]):
         # Extract required fields from config
         pdf_files, pdf_file_filter, output_file = (
             self.config.input_files,
@@ -45,9 +45,6 @@ class PdfToJsonl(TextToJsonl):
 
         # Identify, mark and merge any new entries with previous entries
         with timer("Identify new or updated entries", logger):
-            if not previous_entries:
-                entries_with_ids = list(enumerate(current_entries))
-            else:
             entries_with_ids = TextToJsonl.mark_entries_for_update(
                 current_entries, previous_entries, key="compiled", logger=logger
             )

src/khoj/processor/text_to_jsonl.py

@@ -17,7 +17,7 @@ class TextToJsonl(ABC):
         self.config = config
 
     @abstractmethod
-    def process(self, previous_entries: List[Entry] = None) -> List[Tuple[int, Entry]]:
+    def process(self, previous_entries: List[Entry] = []) -> List[Tuple[int, Entry]]:
         ...
 
     @staticmethod

src/khoj/search_type/text_search.py

@@ -176,10 +176,10 @@ def setup(
 ) -> TextContent:
     # Map notes in text files to (compressed) JSONL formatted file
     config.compressed_jsonl = resolve_absolute_path(config.compressed_jsonl)
-    previous_entries = (
-        extract_entries(config.compressed_jsonl) if config.compressed_jsonl.exists() and not regenerate else None
-    )
-    entries_with_indices = text_to_jsonl(config).process(previous_entries or [])
+    previous_entries = []
+    if config.compressed_jsonl.exists() and not regenerate:
+        previous_entries = extract_entries(config.compressed_jsonl)
+    entries_with_indices = text_to_jsonl(config).process(previous_entries)
 
     # Extract Updated Entries
     entries = extract_entries(config.compressed_jsonl)