Removed checkpoints and issues tracking as it is redundant.

.github/workflows/docs-deploy.yaml

@@ -1,7 +1,7 @@
 name: Deploy docs
 
-# Build the Sphinx site and publish it to GitHub Pages on push to main or dev. Kept separate from
-# ci.yaml (like sync-issues / sync-checkpoints) so CI stays build-and-test only, with no deploy.
+# Build the Sphinx site and publish it to GitHub Pages on push to main or dev. Kept as its own
+# workflow (not a job in ci.yaml) so CI stays build-and-test only, with no deploy.
 on:
   push:
     branches: [main, dev]

AGENTS.md

@@ -9,8 +9,7 @@ Anthropic API.
 
 - Read [`docs/architecture.md`](docs/architecture.md), it is the full design.
 - Read ADRs under [`docs/decisions/`](docs/decisions/), locked decisions live there.
-- Read [`docs/issues.md`](docs/issues.md), work is tracked as phases there.
-- Read [`docs/checkpoints.md`](docs/checkpoints.md), completed work is tracked there.
+- Read the [GitHub issues](https://github.com/sid-ak/study_assistant/issues), work is tracked as phases there.
 - Read [`README.md`](README.md), Status blurb states intent.
 - Compare against repo, which is the ground truth.
   - Scan with `ls` and compare with directory structure in `architecture.md` to gauge progress.
@@ -79,12 +78,12 @@ ADR before changing what it governs, and do not restate its rules here.
 ## PR instructions
 
 - Branch from `dev`, naming the branch with its GitHub issue number first (e.g. `4-embeddings` for
-  issue #4) so `docs/checkpoints.md` attributes correctly.
+  issue #4) so the branch links back to its issue.
 - PR title format: `[<phase or package>] <Title>` — e.g. `[rag_core/store] Add schema + CRUD`.
 - Run the full gate green before handing off (with `docker compose up -d`):
   `uv run ruff check . && uv run ruff format --check . && uv run mypy && uv run pytest && uv run sphinx-build -b html docs site -W`.
-- Update the `README.md` Status blurb in the same change — current status lives there (and in
-  `docs/issues.md` / `docs/checkpoints.md`), not in this file.
+- Update the `README.md` Status blurb in the same change — current status lives there (and in the
+  GitHub issues), not in this file.
 - Never commit; only stage. Do not run `git commit`. At the end of a set of changes, `git add` the
   relevant files and leave them staged for the human to review — but only if 0 files are currently
   staged. If anything is already staged, do not stage at all; leave the working tree as-is.

CONTRIBUTING.md

@@ -34,8 +34,6 @@ pre-commit install      # installs the git hooks
     valid in branch names.)
   - Commit message: prefix with `#<number>` so GitHub auto-links the issue, e.g.
     `#1 add pgvector schema`.
-  - Checkpoint commit messages: `checkpoint: <text>` (optional `#<number>-` prefix). Recorded when
-    the commit is merged into `dev`, not on the feature-branch push.
 
 ## Governance (`AGENTS.md`)
 
@@ -52,7 +50,5 @@ changing direction.
 
 ## Issues / roadmap
 
-Work is tracked as phases on GitHub Issues, which are the source of truth. `docs/issues.md` is an
-auto-generated mirror: the `sync-issues` workflow (`.github/workflows/sync-issues.yaml`) regenerates
-and commits it whenever an issue is opened, closed, edited, or relabeled. Manage issues on GitHub —
-don't hand-edit `docs/issues.md`. Issue bodies are not mirrored.
+Work is tracked as phases on [GitHub Issues](https://github.com/sid-ak/study_assistant/issues),
+which are the source of truth — manage them there.

README.md

@@ -7,7 +7,7 @@ free; only answer generation calls the Anthropic API.
 
 - Design: [`docs/architecture.md`](docs/architecture.md)
 - Decisions: [`docs/decisions/`](docs/decisions/) (ADRs)
-- Roadmap: [`docs/issues.md`](docs/issues.md) (phased)
+- Roadmap: [GitHub issues](https://github.com/sid-ak/study_assistant/issues) (phased)
 
 ## Status