* chore: cleanup benchmarks runner with old flags
* fix tests
* fix: observations rely on source_memory_ids, no link copying
Observations no longer copy any memory_links from their source facts.
Instead, retrieval uses source_memory_ids to traverse:
- Entity connections: observation → source_memory_ids → unit_entities
- Semantic similarity: observations have their own embeddings
- Temporal proximity: observations have their own temporal fields
This avoids data duplication and fixes bidirectionality issues with
entity links being copied to observations.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
* test: update consolidation test for source_memory_ids behavior
Updated test_consolidation_creates_memory_links to test_consolidation_uses_source_memory_ids
to reflect the new behavior where observations use source_memory_ids instead of memory_links
for traversal.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
---------
Co-authored-by: Claude Sonnet 4.5 <noreply@anthropic.com>
* fix: misc fixes for observations and mental models
* feat: improve graph retrieval for observations
- Update LinkExpansionRetriever to traverse through source_memory_ids
for observation entity connections (avoiding data duplication)
- Remove entity link copy from world facts to observations in consolidator
- Add tests for link expansion graph retrieval
- Add directives_applied field to ReflectResult
- Include user's other changes (CLI, docs, client updates)
* fix: CI test failures
- Add mental_model_id parameter to create_mental_model function
- Fix ToolCallTrace not including reason field from ToolCall
- Improve test_link_expansion_observation_graph_retrieval to wait for consolidation with retry
* chore: reduce link expansion log verbosity
* Revert "chore: reduce link expansion log verbosity"
This reverts commit 3ce759391cead1012157785fa78fef16ef9bfe3b.
* feat: add semantic/temporal/entity links as fallback in graph retrieval
- Add fallback query for semantic, temporal, and entity links from memory_links
- Check both directions (outgoing and incoming links)
- Weight fallback results at 0.5x to prioritize entity links via unit_entities
- Fixes graph retrieval returning 0 when data has cross-cluster temporal connections
* fix: enable observations fixture for link expansion test
- Add enable_observations fixture to ensure observations are created
- Increase wait time from 10 to 30 seconds for CI reliability
* misc: add mcp integration tests and increase test coverage
* misc: add mcp integration tests and increase test coverage
* misc: add mcp integration tests and increase test coverage
* bump pg0 0.11.x and improve documentation
* bump pg0 0.11.x and improve documentation
* bump pg0 0.11.x and improve documentation
* ci: test notebooks on ci
* ci: test notebooks on ci
* rm llms-full from repo
* formatting
* formatting
