refactor: replace Mongo and Redis/BullMQ with SQLite-backed stores

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -1,5 +1,5 @@
 name: Bug report
-description: Something in bytebell-server or the bytebell CLI is broken or behaving unexpectedly.
+description: Something in plumbline-server or the plumbline CLI is broken or behaving unexpectedly.
 title: "[bug] "
 labels: ["bug", "needs-triage"]
 body:
@@ -8,15 +8,15 @@ body:
       value: |
         Thanks for taking the time to file a bug! A few quick tips:
         - Please redact API keys, tokens, and private repo URLs from anything you paste.
-        - Server and CLI logs live in `~/.bytebell/logs/`.
+        - Server and CLI logs live in `~/.plumbline/logs/`.
         - Only the first four fields are required — fill in the rest if you have it handy.
 
   - type: textarea
     id: summary
     attributes:
       label: What happened?
       description: A short description of the bug. What did you do, and what went wrong?
-      placeholder: I ran `bytebell index https://github.com/...` and the worker stalled at PROCESSING.
+      placeholder: I ran `plumbline index https://github.com/...` and the worker stalled at PROCESSING.
     validations:
       required: true
 
@@ -26,8 +26,8 @@ body:
       label: Steps to reproduce
       description: The minimum sequence of commands or clicks needed to see the bug.
       placeholder: |
-        1. `bytebell boot`
-        2. `bytebell index <repo-url>`
+        1. `plumbline boot`
+        2. `plumbline index <repo-url>`
         3. Wait ~2 minutes
     validations:
       required: true
@@ -42,25 +42,25 @@ body:
   - type: input
     id: version
     attributes:
-      label: Bytebell version
-      description: Output of `bytebell --version`.
+      label: Plumbline version
+      description: Output of `plumbline --version`.
       placeholder: e.g. 0.4.2
     validations:
       required: true
 
   - type: dropdown
     id: component
     attributes:
-      label: Which part of Bytebell is affected?
+      label: Which part of Plumbline is affected?
       description: Pick whatever feels closest — "Not sure" is fine.
       multiple: true
       options:
         - "Not sure"
-        - "bytebell-server (HTTP / MCP / workers)"
-        - "bytebell CLI / TUI"
+        - "plumbline-server (HTTP / MCP / workers)"
+        - "plumbline CLI / TUI"
         - "Ingestion (@bb/ingest-github)"
         - "MCP surface (@bb/mcp)"
-        - "Adapter (@bb/mongo / @bb/neo4j / @bb/redis)"
+        - "Adapter (@bb/sqlite / @bb/neo4j)"
         - "LLM layer (@bb/llm)"
         - "Config / first-run setup (@bb/config)"
         - "Docs / README"
@@ -90,7 +90,7 @@ body:
     id: logs
     attributes:
       label: Logs or error output
-      description: Paste relevant lines from `~/.bytebell/logs/server-YYYY-MM-DD.log` or `cli-YYYY-MM-DD.log`. Redact secrets.
+      description: Paste relevant lines from `~/.plumbline/logs/server-YYYY-MM-DD.log` or `cli-YYYY-MM-DD.log`. Redact secrets.
       render: shell
 
   - type: textarea

.github/ISSUE_TEMPLATE/feature_request.yml

@@ -1,5 +1,5 @@
 name: Feature request
-description: Suggest a new capability or improvement for Bytebell.
+description: Suggest a new capability or improvement for Plumbline.
 title: "[feat] "
 labels: ["enhancement", "needs-triage"]
 body:

.gitleaks.toml

@@ -1,4 +1,4 @@
-title = "Bytebell-public gitleaks config"
+title = "Plumbline-public gitleaks config"
 
 [extend]
 useDefault = true

CHANGELOG.md

@@ -1,23 +1,50 @@
 # Changelog
 
-All notable changes to Bytebell are documented in this file. The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+All notable changes to Plumbline are documented in this file. The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 ## [Unreleased]
 
+### Changed
+
+- **The document store is now SQLite.** MongoDB is removed: the `mongo` container is
+  gone from `infra/docker/docker-compose.yml`, and `~/.plumbline/data.sqlite` holds the
+  knowledge documents, raw file rows, activity, usage, and the concept-graph enrichment
+  ledger.
+- Existing installs upgrade in place: a `config.json` carrying `db_provider: "mongo"` is
+  migrated to `sqlite` on read, and the retired `mongo_uri` key is dropped from the file
+  on the next config write. **Data is not migrated** — repositories indexed against
+  MongoDB must be re-indexed.
+- **The job queue is now SQLite too.** Redis and BullMQ are removed: the job queue is
+  Honker over SQLite (`~/.plumbline/queue.db`) in every configuration, so the `redis`
+  container is gone from `infra/docker/docker-compose.yml`. A stored
+  `queue_provider: "bullmq"` migrates to `honker` on read, and the retired `redis_url`
+  key is dropped from `config.json`. **In-flight jobs are not migrated** — drain or
+  re-submit anything queued before the upgrade.
+- Neo4j is now the only container `plumbline boot` starts.
+- `DELETE /api/v1/repos/<knowledgeId>` renames its `mongoDeleted` response field to
+  `dbDeleted`.
+
+### Removed
+
+- The `@bb/mongo` package, the `mongo_uri` config key, and the `mongo` value of
+  `db_provider`.
+- The `@bb/redis` and `@bb/queue-bullmq` packages, the `redis_url` config key, the
+  `bullmq` value of `queue_provider`, and the `Redis*` error classes.
+
 ## [0.1.0] — 2026-05-08
 
 ### Added
 
 - Initial public release.
-- `bytebell-server` HTTP daemon (Express 5) with ingestion routes (`/api/v1/...`) and MCP transport (`/mcp`, HTTP + SSE).
-- `bytebell` CLI (Ink/React TUI + commander) with subcommands: `boot`, `index`, `ingest`, `pull`, `ls`, `delete`, `set`, `server`, `shutdown`, `stats`, `mcp`.
+- `plumbline-server` HTTP daemon (Express 5) with ingestion routes (`/api/v1/...`) and MCP transport (`/mcp`, HTTP + SSE).
+- `plumbline` CLI (Ink/React TUI + commander) with subcommands: `boot`, `index`, `ingest`, `pull`, `ls`, `delete`, `set`, `server`, `shutdown`, `stats`, `mcp`.
 - GitHub repository ingestion via `BasicFileAnalysisStrategy` (file-walk + per-file LLM analysis).
 - MCP retrieval tools: `smart_search`, `keyword_lookup`, `retrieve_file` .
-- Token-usage telemetry persisted to MongoDB (`mcp_activity`, `usage_summary`); live USD estimate against OpenRouter pricing via `bytebell stats`.
+- Token-usage telemetry persisted to MongoDB (`mcp_activity`, `usage_summary`); live USD estimate against OpenRouter pricing via `plumbline stats`.
 - Local-first single-tenant architecture (`orgId="local"`); BYO MongoDB + Neo4j + Redis.
-- Configuration via `~/.bytebell/config.json` (no `.env`), managed through `bytebell set <key> <value>`.
+- Configuration via `~/.plumbline/config.json` (no `.env`), managed through `plumbline set <key> <value>`.
 - BullMQ in-process workers with retryable, idempotent jobs.
-- Winston structured logging to `~/.bytebell/logs/` plus stdout.
+- Winston structured logging to `~/.plumbline/logs/` plus stdout.
 
 ### License