Feature/backlog work (#2)

* Add Dijkstra shortest path and degree centrality graph algorithms

- dijkstra(source, target) finds shortest path between nodes
- degreeCentrality() calculates in/out/total degree for all nodes
- Modularize graph algorithm code into separate files for maintainability
- Add Python and Rust bindings with full test coverage

* Add Leiden community detection to Python bindings

- leiden_communities() method uses graspologic for high-quality community detection
- to_rustworkx() method exports graph to rustworkx PyDiGraph format
- Optional dependencies: pip install graphqlite[leiden] or graphqlite[rustworkx]

* Add graph algorithms, fix OPTIONAL MATCH transformation, add modulo operator

Graph Algorithms:
- Eigenvector centrality with power iteration
- Betweenness centrality
- Closeness centrality
- Triangle counting and clustering coefficient
- Connected components (weak and strong)
- All-pairs shortest path (Floyd-Warshall)
- A* pathfinding with heuristics
- K-nearest neighbors
- Louvain community detection
- Graph similarity (Jaccard, cosine, overlap)
- BFS/DFS traversal

Bug Fixes:
- Fix OPTIONAL MATCH transformation generating duplicate LEFT JOINs by checking
  sql_builder.from_clause and join_clauses in addition to sql_buffer
- Fix eigenvector centrality test using symmetric graph that produces uniform scores

New Features:
- Add modulo operator (%) support to Cypher expressions

Bindings:
- Refactor Python bindings into modular graph/ and algorithms/ packages
- Refactor Rust bindings into modular graph/ and algorithms/ modules
- Add comprehensive test coverage for new algorithms

* Implement REMOVE clause for property and label removal

Add executor support for REMOVE clause operations:
- Remove node properties (REMOVE n.prop)
- Remove multiple properties (REMOVE n.a, n.b)
- Remove node labels (REMOVE n:Label)
- Remove edge properties (REMOVE r.prop)

Includes schema functions for property/label deletion and
comprehensive tests across CUnit, functional SQL, Rust, and
Python bindings.

* Return empty array for zero-row MATCH results

MATCH queries with no matching rows now return [] instead of a
success message, aligning with standard Cypher semantics. Modification
queries (CREATE, DELETE, etc.) without RETURN clauses continue to
show statistics.

Also fixes REMOVE tests to check for null string values rather than
NULL pointers.

* Implement IN membership operator for list checking

Add support for `expr IN [list]` syntax to check if a value exists
in a list:
- `5 IN [1, 2, 5, 10]` returns true
- `'x' IN ['a', 'b', 'c']` returns false
- `MATCH (n) WHERE n.status IN ['active', 'pending'] RETURN n`

Uses %dprec to disambiguate between IN operator in list literals
vs list comprehension syntax `[x IN list]`.

Includes tests for Python and Rust bindings.

* Implement STARTS WITH, ENDS WITH, CONTAINS string operators

Add infix string matching operators as specified by OpenCypher:
- STARTS WITH: checks if string begins with prefix
- ENDS WITH: checks if string ends with suffix
- CONTAINS: checks if string contains substring

Transform to SQL:
- STARTS WITH → str LIKE prefix || '%'
- ENDS WITH → str LIKE '%' || suffix
- CONTAINS → INSTR(str, substr) > 0

Also supports function call syntax (contains(), startsWith(), endsWith())
for backward compatibility.

* Fix OPTIONAL MATCH, UNWIND+CREATE, and array index bugs

- OPTIONAL MATCH now correctly uses LEFT JOIN semantics instead of
  producing cartesian products. Routes multi-MATCH queries through
  the transform pipeline to properly process all clauses.

- UNWIND+CREATE now iterates correctly over list elements instead
  of only creating a single node.

- Array index syntax (list[0]) now supported in expressions via
  new subscript operator handling in the parser and transform.

- Added comprehensive test files for expanded Cypher coverage
  (expressions, clauses, patterns, functions, predicates).

* Bump version to 0.1.0-beta.4

---------

Co-authored-by: Dylan Storey <dstorey@gmail.com>

Author: dylanbstorey

.metis/backlog/bugs/GQLITE-T-0003.md …s/archived/backlog/bugs/GQLITE-T-0003.md.metis/backlog/bugs/GQLITE-T-0003.md renamed to .metis/archived/backlog/bugs/GQLITE-T-0003.md .metis/backlog/bugs/GQLITE-T-0003.md renamed to .metis/archived/backlog/bugs/GQLITE-T-0003.md

@@ -7,7 +7,7 @@ created_at: 2025-12-24T01:49:48.647722+00:00
 updated_at: 2025-12-24T02:07:01.517901+00:00
 parent: 
 blocked_by: []
-archived: false
+archived: true
 
 tags:
   - "#task"
@@ -44,6 +44,8 @@ Fix parameter binding (`$param`) support in WHERE clauses and other expressions.
 
 ## Acceptance Criteria
 
+## Acceptance Criteria
+
 - [ ] `MATCH (n) WHERE n.name = $name RETURN n` parses and transforms successfully
 - [ ] Parameters work in WHERE clause comparisons
 - [ ] Parameters work in property maps: `CREATE (n:Person {name: $name})`

.metis/backlog/bugs/GQLITE-T-0011.md …s/archived/backlog/bugs/GQLITE-T-0011.md.metis/backlog/bugs/GQLITE-T-0011.md renamed to .metis/archived/backlog/bugs/GQLITE-T-0011.md .metis/backlog/bugs/GQLITE-T-0011.md renamed to .metis/archived/backlog/bugs/GQLITE-T-0011.md

@@ -7,7 +7,7 @@ created_at: 2025-12-24T14:16:05.505777+00:00
 updated_at: 2025-12-24T14:38:27.912817+00:00
 parent: 
 blocked_by: []
-archived: false
+archived: true
 
 tags:
   - "#task"
@@ -68,6 +68,8 @@ Fix the Cypher executor to return node objects as separate rows instead of seria
 
 ## Acceptance Criteria
 
+## Acceptance Criteria
+
 ## Acceptance Criteria **[REQUIRED]**
 
 - [ ] `MATCH (n) RETURN n` returns each node as a separate row

.metis/backlog/features/GQLITE-T-0001.md …chived/backlog/features/GQLITE-T-0001.md.metis/backlog/features/GQLITE-T-0001.md renamed to .metis/archived/backlog/features/GQLITE-T-0001.md .metis/backlog/features/GQLITE-T-0001.md renamed to .metis/archived/backlog/features/GQLITE-T-0001.md

@@ -7,7 +7,7 @@ created_at: 2025-12-24T01:49:48.401416+00:00
 updated_at: 2025-12-24T02:26:57.086473+00:00
 parent: 
 blocked_by: []
-archived: false
+archived: true
 
 tags:
   - "#task"
@@ -42,6 +42,8 @@ Add support for UNION and UNION ALL operators to combine results from multiple q
 
 ## Acceptance Criteria
 
+## Acceptance Criteria
+
 - [ ] `RETURN 1 AS x UNION RETURN 2 AS x` returns two rows
 - [ ] `RETURN 1 AS x UNION ALL RETURN 1 AS x` returns two identical rows
 - [ ] UNION removes duplicates, UNION ALL keeps all rows

.metis/backlog/features/GQLITE-T-0002.md …chived/backlog/features/GQLITE-T-0002.md.metis/backlog/features/GQLITE-T-0002.md renamed to .metis/archived/backlog/features/GQLITE-T-0002.md .metis/backlog/features/GQLITE-T-0002.md renamed to .metis/archived/backlog/features/GQLITE-T-0002.md

@@ -7,7 +7,7 @@ created_at: 2025-12-24T01:49:48.522655+00:00
 updated_at: 2025-12-24T02:41:12.493315+00:00
 parent: 
 blocked_by: []
-archived: false
+archived: true
 
 tags:
   - "#task"
@@ -42,6 +42,8 @@ Support multiple labels on nodes using the `(:Label1:Label2)` syntax, allowing n
 
 ## Acceptance Criteria
 
+## Acceptance Criteria
+
 - [ ] `CREATE (n:Person:Employee {name: "Alice"})` creates node with both labels
 - [ ] `MATCH (n:Person:Employee)` matches only nodes with BOTH labels
 - [ ] `MATCH (n:Person)` matches nodes that have Person label (even if they have others)

.metis/backlog/features/GQLITE-T-0004.md …chived/backlog/features/GQLITE-T-0004.md.metis/backlog/features/GQLITE-T-0004.md renamed to .metis/archived/backlog/features/GQLITE-T-0004.md .metis/backlog/features/GQLITE-T-0004.md renamed to .metis/archived/backlog/features/GQLITE-T-0004.md

@@ -7,7 +7,7 @@ created_at: 2025-12-24T01:49:48.772403+00:00
 updated_at: 2025-12-24T02:49:08.449297+00:00
 parent: 
 blocked_by: []
-archived: false
+archived: true
 
 tags:
   - "#task"
@@ -42,6 +42,8 @@ Implement the REMOVE clause for deleting properties from nodes and relationships
 
 ## Acceptance Criteria
 
+## Acceptance Criteria
+
 - [ ] `MATCH (n) REMOVE n.property RETURN n` removes the property
 - [ ] `MATCH (n) REMOVE n:Label RETURN n` removes the label from the node
 - [ ] Multiple removes in one clause: `REMOVE n.a, n.b, n:Label`

.metis/backlog/features/GQLITE-T-0005.md …chived/backlog/features/GQLITE-T-0005.md.metis/backlog/features/GQLITE-T-0005.md renamed to .metis/archived/backlog/features/GQLITE-T-0005.md .metis/backlog/features/GQLITE-T-0005.md renamed to .metis/archived/backlog/features/GQLITE-T-0005.md

@@ -7,7 +7,7 @@ created_at: 2025-12-24T01:49:48.904017+00:00
 updated_at: 2025-12-24T02:54:59.590287+00:00
 parent: 
 blocked_by: []
-archived: false
+archived: true
 
 tags:
   - "#task"
@@ -42,6 +42,8 @@ Add the regex matching operator (`=~`) for pattern matching on string properties
 
 ## Acceptance Criteria
 
+## Acceptance Criteria
+
 - [ ] `MATCH (n) WHERE n.name =~ "A.*" RETURN n` matches names starting with A
 - [ ] `MATCH (n) WHERE n.email =~ ".*@gmail.com" RETURN n` matches Gmail addresses
 - [ ] Case-sensitive matching by default

.metis/backlog/features/GQLITE-T-0006.md …chived/backlog/features/GQLITE-T-0006.md.metis/backlog/features/GQLITE-T-0006.md renamed to .metis/archived/backlog/features/GQLITE-T-0006.md .metis/backlog/features/GQLITE-T-0006.md renamed to .metis/archived/backlog/features/GQLITE-T-0006.md

@@ -7,7 +7,7 @@ created_at: 2025-12-24T01:49:49.042048+00:00
 updated_at: 2025-12-24T15:02:17.022679+00:00
 parent: 
 blocked_by: []
-archived: false
+archived: true
 
 tags:
   - "#task"
@@ -42,6 +42,8 @@ Implement the FOREACH clause for iterating over a list and performing update ope
 
 ## Acceptance Criteria
 
+## Acceptance Criteria
+
 - [ ] `FOREACH (x IN [1,2,3] | CREATE (n {val: x}))` creates 3 nodes
 - [ ] `FOREACH (n IN nodes | SET n.updated = true)` updates all nodes in list
 - [ ] Nested FOREACH supported

.metis/backlog/features/GQLITE-T-0007.md …chived/backlog/features/GQLITE-T-0007.md.metis/backlog/features/GQLITE-T-0007.md renamed to .metis/archived/backlog/features/GQLITE-T-0007.md .metis/backlog/features/GQLITE-T-0007.md renamed to .metis/archived/backlog/features/GQLITE-T-0007.md

@@ -7,7 +7,7 @@ created_at: 2025-12-24T01:49:49.189917+00:00
 updated_at: 2025-12-24T03:14:18.058281+00:00
 parent: 
 blocked_by: []
-archived: false
+archived: true
 
 tags:
   - "#task"
@@ -42,6 +42,8 @@ Implement LOAD CSV clause for importing data from CSV files into the graph datab
 
 ## Acceptance Criteria
 
+## Acceptance Criteria
+
 - [ ] `LOAD CSV FROM "file.csv" AS row CREATE (n {name: row[0]})`
 - [ ] `LOAD CSV WITH HEADERS FROM "file.csv" AS row CREATE (n {name: row.name})`
 - [ ] Support for local file paths

.metis/backlog/features/GQLITE-T-0010.md …chived/backlog/features/GQLITE-T-0010.md.metis/backlog/features/GQLITE-T-0010.md renamed to .metis/archived/backlog/features/GQLITE-T-0010.md .metis/backlog/features/GQLITE-T-0010.md renamed to .metis/archived/backlog/features/GQLITE-T-0010.md

@@ -7,7 +7,7 @@ created_at: 2025-12-24T05:18:53.733240+00:00
 updated_at: 2025-12-24T15:06:43.265133+00:00
 parent: 
 blocked_by: []
-archived: false
+archived: true
 
 tags:
   - "#task"
@@ -72,6 +72,8 @@ Graph algorithms (PageRank, Label Propagation, Betweenness Centrality) currently
 
 ## Acceptance Criteria
 
+## Acceptance Criteria
+
 ## Acceptance Criteria **[REQUIRED]**
 
 - [ ] `pagerank()` returns both `node_id` (rowid) and `user_id` (property) columns

.metis/backlog/features/GQLITE-T-0012.md …chived/backlog/features/GQLITE-T-0012.md.metis/backlog/features/GQLITE-T-0012.md renamed to .metis/archived/backlog/features/GQLITE-T-0012.md .metis/backlog/features/GQLITE-T-0012.md renamed to .metis/archived/backlog/features/GQLITE-T-0012.md

@@ -7,7 +7,7 @@ created_at: 2025-12-24T14:18:38.677564+00:00
 updated_at: 2025-12-24T15:02:39.854072+00:00
 parent: 
 blocked_by: [GQLITE-T-0011]
-archived: false
+archived: true
 
 tags:
   - "#task"
@@ -58,6 +58,8 @@ Complete the nanographrag demo to showcase GraphQLite + sqlite-vec for knowledge
 
 ## Acceptance Criteria
 
+## Acceptance Criteria
+
 ## Acceptance Criteria **[REQUIRED]**
 
 - [x] Entity extraction with spaCy NER (181 entities, 266 relationships from 19 docs)