Schema drift detection and pruning (detect-schema-drift, prune-schema) #88

Schema drift detection and pruning

Tracking issue for the stacked PRs that add schema drift detection and pruning. A declared concept or property with zero instances in the graph is "unused"; after documents are deleted and synced the schema never shrinks.

Commands

• mykg detect-schema-drift --session S: read-only report, recorded to intermediate/schema_drift.json.
• mykg prune-schema --session S [--preview | --plan FILE]: preview writes an editable plan file; apply backs up schema.json, prunes, records a schema_prune history entry, regenerates schema.ttl and flattened_schema.json, then refreshes outputs via validate_graph. Nodes and edges are never edited. No LLM calls, no new config keys, not a pipeline step.

Stacked PRs (merge in this order)

• feat: schema drift core analyzer, prune plan and apply (1/5) #83 core analyzer, prune plan and apply (base main)
• feat: detect-schema-drift and prune-schema CLI commands (unit 2/5) #84 CLI commands (base: feat: schema drift core analyzer, prune plan and apply (1/5) #83 branch)
• feat: walkthrough Schema Health section (schema drift 3/5) #85 walkthrough "Schema Health" section (base: feat: detect-schema-drift and prune-schema CLI commands (unit 2/5) #84 branch)
• feat: mykg_schema_drift MCP tool (schema drift 4/5) #86 MCP tool mykg_schema_drift (base: feat: walkthrough Schema Health section (schema drift 3/5) #85 branch)
• docs: schema drift detection and pruning (unit 5/5) #87 docs and skill (base: feat: mykg_schema_drift MCP tool (schema drift 4/5) #86 branch)

Review outcome

All Sourcery review comments were triaged and the fixes pushed to each PR. Declined: cross-process locking, moving the MCP scan to a thread, regenerating knowledge_graph.ttl in core. Refuted: the claim that grow-schema sessions lock every schema entry.

Known gaps

• schema.pre_prune.json is overwritten on each prune (single backup).
• Writes are ordered but not one transaction; re-running a prune is idempotent and approve-schema repairs schema.ttl.
• Lock-file loading is duplicated between cli.py and walkthrough.py.
• Suggested commands use POSIX shell quoting only.
• The tier-4 "grace-period decay" is not implemented.