feat(memory): add memory extension with core functionality and tests

- Implemented MemoryStore class for managing concepts with YAML frontmatter.
- Added methods for creating, reading, updating, and deleting concepts.
- Introduced locking mechanism for concurrent access.
- Developed search and hinting capabilities for concept retrieval.
- Created tests for access control and store functionality.
- Added long-term memory skill documentation and operational guidelines.
- Included package.json and package-lock.json for dependency management.

skills/long-term-memory/SKILL.md

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+---
+name: long-term-memory
+description: Use Kimiko's durable OKF memory when the user asks to remember, forget, or recall something; refers to prior conversations; asks about a known person, project, preference, or decision; states a durable correction or preference; or says something is off the record. Do not use for current-turn-only facts.
+---
+
+# Long-term memory
+
+## Decision table
+
+| Situation | Action |
+|---|---|
+| Explicit “remember this” | Search for duplicates; read a matching concept; then write. |
+| Explicit recall or “what do you remember?” | Search, then read only relevant concepts. |
+| Reference to an earlier conversation | Search before answering. |
+| Stable preference or correction | Ask whether to remember it unless storage was explicitly requested. |
+| Confirmed long-lived project decision | Offer to remember it. |
+| New information conflicts with memory | Clarify; never silently overwrite. |
+| Transient task, speculation, or casual remark | Do not store. |
+| Credential, secret, or sensitive fact | Do not store without an explicit informed request. |
+| “Don’t remember this” or “off the record” | Do not store it. |
+| Explicit forget request | Search, read, then forget with exact-ID confirmation. |
+
+Store only information likely to matter in another session, sufficiently stable, and explicitly requested or confirmed.
+
+## Workflow
+
+1. Call `memory_search` in the current user turn. Retrieval hints do not replace this step.
+2. Call `memory_read` only for relevant IDs. Existing concepts must be read before update or deletion.
+3. Write one coherent concept with `memory_write`; update an existing ID rather than duplicating it.
+4. Use structured Markdown and explicit links such as `[Atlas](/projects/atlas.md)`.
+5. After mutation, tell the user briefly which concept was created, updated, or forgotten.
+
+Never author frontmatter, timestamps, indexes, or logs. The extension generates, validates, repairs, and verifies them deterministically.
+
+For diagnostics and recovery policy, read [operations.md](references/operations.md).

skills/long-term-memory/references/operations.md

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+# Memory operations
+
+## Storage
+
+The OKF bundle is `${PI_CODING_AGENT_DIR}/memory`. Concept IDs are lowercase bundle-relative paths without `.md`. `index.md` and `log.md` are reserved.
+
+## Commands
+
+- `/memory-path` — show the bundle path.
+- `/memory-check` — report structural problems without modifying concepts.
+- `/memory-check --repair` — repair deterministically and regenerate indexes.
+
+## Turn-scoped access
+
+Each user turn clears prior search/read authorization and removes detailed memory tools. Explicit memory language may reveal the tools early, and `memory_search` enables them otherwise; visibility never bypasses the workflow gate. Existing concepts must be returned by search and read in that same turn before mutation. Metadata-only retrieval hints are injected through the ephemeral per-turn system prompt, never session messages, so previous hints do not accumulate.
+
+## Repair policy
+
+- Missing/invalid timestamps use the file's modification time; the model never supplies them.
+- Missing types become `Recovered Concept`.
+- Invalid or absent frontmatter is backed up under `memory/.recovery/`, then replaced with valid metadata while retaining the recoverable body.
+- Generated index sections are replaced between marker comments; human text outside the markers is retained.
+- Writes use a bundle lock, atomic rename, read-after-write semantic verification, and one deterministic retry.
+- No-op writes retain the prior timestamp and do not create a log entry.
+
+Inspect any concept carrying `repair_backup` because malformed metadata may require human review. The bundle is ignored by Git by default; opt into private versioning only with an explicit retention and deletion policy. The extension never auto-commits.