diff --git a/.gitignore b/.gitignore
index 431ffbf..aa35b9b 100644
--- a/.gitignore
+++ b/.gitignore
@@ -175,7 +175,6 @@ templates
 /prepared
 /Lab9_out*
 *.fish
-!scripts/update-notes.fish
 .scriptmark_extracted/
 .remember/
 tests/geec/
@@ -183,11 +182,11 @@ tests_submission/
 
 # P-669 test fixtures — the broad rules above (*.csv, submissions, templates, config.toml)
 # must not swallow committed test data.
-!crates/scriptmark/tests/fixtures/**
+!src/crates/scriptmark/tests/fixtures/**
 # ...but not what running the suite over them produces.
-crates/scriptmark/tests/fixtures/**/__pycache__/
-crates/scriptmark/tests/fixtures/**/.scriptmark_extracted/
-crates/scriptmark/tests/fixtures/**/.DS_Store
+src/crates/scriptmark/tests/fixtures/**/__pycache__/
+src/crates/scriptmark/tests/fixtures/**/.scriptmark_extracted/
+src/crates/scriptmark/tests/fixtures/**/.DS_Store
 
 # P-674 example bundles ship their students; `submissions` above would drop them.
 !examples/bundles/*/submissions/
diff --git a/CLAUDE.md b/CLAUDE.md
index 80e2e5c..1dc98ff 100644
--- a/CLAUDE.md
+++ b/CLAUDE.md
@@ -7,30 +7,39 @@ This file provides guidance to Claude Code (claude.ai/code) when working with co
 `CLAUDE.md` is the canonical project instruction file; `AGENTS.md` and
 `.github/copilot-instructions.md` are symlinks to it.
 
-- Documentation is in the `notes/` git submodule:
+- Public documentation belongs in `docs/`. Private documentation is in the `notes/` git submodule:
   `https://github.com/Acture/obsidian-vault.git`, branch `project/scriptmark`.
   Start at `notes/README.md`; the teacher contract is
   `notes/docs/test-bundles.md`, and plans are in
-  `notes/docs/plans/`. Do not recreate a maintained root `docs/` tree.
+  `notes/docs/plans/`. Do not copy private notes into the public documentation tree.
+  The project branch root contains only this project's notes; the vault's `master`
+  places them under `scriptmark/`. Keep shared automation and vault configuration on master.
 - Default to the latest remote `project/scriptmark` notes. At the start of every
-  session, after pulling code, and before reading or editing notes, run
-  `fish scripts/update-notes.fish` from this repository. This initializes missing
-  notes, fetches the configured project branch, fast-forwards it and leaves that branch
-  checked out. It handles single-branch clones. Never assume the gitlink is the latest.
+  session, after pulling code, and before reading or editing notes, follow the native
+  Git update sequence in README's "Documentation and checkout" section. It explicitly
+  fetches the project branch, checks for local work, switches to `project/scriptmark`
+  and fast-forwards it. It handles single-branch clones. Never assume the gitlink is latest.
 - Clone with `git clone https://github.com/Acture/scriptmark.git`, enter the clone,
-  then run the same helper. It stops on local notes edits, unpushed commits or divergence;
-  preserve and reconcile them instead of resetting or force-pushing. If fetching fails,
-  report that the latest notes were not verified; do not silently describe stale notes as current.
-- Edit only `notes/`. A newer notes checkout can make the parent's gitlink
+  then initialize with `git submodule update --init --remote --no-single-branch -- notes`
+  and `git -C notes switch project/scriptmark`. For existing notes, use the guarded
+  update sequence instead. Stop on local edits, unpushed commits or divergence; preserve
+  and reconcile them instead of resetting or force-pushing. If fetching fails, report
+  that the latest notes were not verified; do not describe stale notes as current.
+  Shared synchronization and submission tooling belongs to the notes repository;
+  do not add a project-local notes updater.
+- Edit private documentation only in `notes/`. A newer notes checkout can make the parent's gitlink
   dirty; review `git diff --submodule=log -- notes` and include the updated reference in
   the next code commit. Do not reset notes just to remove that expected difference.
 - The gitlink remains a concrete saved checkpoint because Git requires one. Use
   `git submodule update --init --checkout -- notes` only for an explicitly requested
   historical reproduction, with clean notes. Pinned checkout is not the daily workflow.
-- Stage with `git -C notes add README.md`, commit in `notes`, and push with
-  `python3 (git -C notes rev-parse --path-format=absolute --git-common-dir)/hooks/notes-boundary/submit_project.py --repo notes`. Only after that push
-  succeeds, stage `notes` in this repository and commit/push its new gitlink. A failed
-  push must never leave a published parent pointer to unavailable notes.
+- Stage specific documents in `notes/` and commit there. Publish with the master-owned
+  `hooks/notes-boundary/submit_project.py --repo notes` under the notes repository's
+  common Git directory; it runs the required remote check before pushing that SHA.
+  The remote requires `notes-boundary/root/scriptmark` from GitHub Actions.
+  Install/update this helper from the notes repository's trusted `origin/master` as
+  shown in README. Direct pushes of unchecked commits are rejected. Only after a
+  successful submission, stage `notes` here and commit/push its new gitlink.
 - The README contains the complete command sequence. Keep original histories and
   resolve divergence without overwriting either side.
 - Linear is the execution home. Keep runnable examples, code, measurements and raw
@@ -62,6 +71,11 @@ default Python is newer than the PyO3 version supports; see the P-676 validation
 
 Single `scriptmark` crate (lib + bin) with `scriptmark-py` as separate cdylib for PyO3.
 
+All product source is under `src/`: Rust packages live in `src/crates/` and the
+Python package entry point in `src/python/scriptmark/`. Workspace/build configuration
+stays at the repository root, where Cargo and Maturin commands are run. The module
+paths below are relative to `src/crates/scriptmark/src/`.
+
 Data flows: TOML specs + student files → Runner → grading record (evidence + score
 revisions) → Display/DB/HTML/Canvas. `rescore` adds a revision from saved evidence.
 
@@ -96,21 +110,21 @@ Zero and withheld grades stay distinct. See the notes' teacher contract for poli
 
 ## Critical Files
 
-- `crates/scriptmark/src/runner/python.rs` — PythonExecutor + embedded helper scripts (HELPER_SCRIPT, CHAIN_HELPER_SCRIPT). Contains import allowlist, env sanitization, `sandboxed_cmd()`, `spawn_with_timeout()`.
-- `crates/scriptmark/src/runner/sandbox.rs` — SandboxConfig + setrlimit application. Platform-conditional: RLIMIT_AS skipped on macOS, RLIMIT_* constants differ between Linux (c_uint) and macOS (c_int).
-- `crates/scriptmark/src/runner/orchestrator.rs` — Runs vars→setup→expand→oracle→execute pipeline per student, tokio parallel.
-- `crates/scriptmark/src/models/spec.rs` — All TOML spec structs (TestSpec, TestCase, SetupStep, Parametrize, Oracle, LintConfig, CheckMethod).
-- `crates/scriptmark/src/discovery.rs` — File discovery + ZIP archive extraction with size/count limits.
-- `crates/scriptmark/src/record.rs` — The grading record every consumer reads (`--output`): evidence with submission/spec fingerprints, append-only score revisions, `check()` refusing evidence whose tests, submissions or matching changed.
-- `crates/scriptmark/src/grading.rs` — GradingPolicy dispatch (templates + Rhai formulas).
-- `crates/scriptmark/src/main.rs` — All CLI command handlers.
-- `crates/scriptmark-py/src/lib.rs` — PyO3 bindings: grade(), run(), discover(), load_spec(), StudentResult, TestSpec classes.
+- `src/crates/scriptmark/src/runner/python.rs` — PythonExecutor + embedded helper scripts (HELPER_SCRIPT, CHAIN_HELPER_SCRIPT). Contains import allowlist, env sanitization, `sandboxed_cmd()`, `spawn_with_timeout()`.
+- `src/crates/scriptmark/src/runner/sandbox.rs` — SandboxConfig + setrlimit application. Platform-conditional: RLIMIT_AS skipped on macOS, RLIMIT_* constants differ between Linux (c_uint) and macOS (c_int).
+- `src/crates/scriptmark/src/runner/orchestrator.rs` — Runs vars→setup→expand→oracle→execute pipeline per student, tokio parallel.
+- `src/crates/scriptmark/src/models/spec.rs` — All TOML spec structs (TestSpec, TestCase, SetupStep, Parametrize, Oracle, LintConfig, CheckMethod).
+- `src/crates/scriptmark/src/discovery.rs` — File discovery + ZIP archive extraction with size/count limits.
+- `src/crates/scriptmark/src/record.rs` — The grading record every consumer reads (`--output`): evidence with submission/spec fingerprints, append-only score revisions, `check()` refusing evidence whose tests, submissions or matching changed.
+- `src/crates/scriptmark/src/grading.rs` — GradingPolicy dispatch (templates + Rhai formulas).
+- `src/crates/scriptmark/src/main.rs` — All CLI command handlers.
+- `src/crates/scriptmark-py/src/lib.rs` — PyO3 bindings: grade(), run(), discover(), load_spec(), StudentResult, TestSpec classes.
 
 ## Conventions
 
 - Workspace dependencies in root `Cargo.toml`, crates reference with `{ workspace = true }`
 - `thiserror` for library error types, `anyhow` for CLI/binary error handling
-- All checkers implement `Checker` trait in `crates/scriptmark/src/checker/mod.rs`
+- All checkers implement `Checker` trait in `src/crates/scriptmark/src/checker/mod.rs`
 - Integration tests spawn real Python processes — need `python3` available
 - `scriptmark-py` has `publish = false` (cdylib, distributed via PyPI/maturin, not crates.io)
 - Platform-specific code uses `#[cfg(target_os = "macos")]` / `#[cfg(target_os = "linux")]` for rlimit types
@@ -150,19 +164,3 @@ seed = 42
 [cases.parametrize.oracle]
 rhai = "if a >= b { a } else { b }"
 ```
-
-
-## Project notes submission
-
-`docs/` is reserved for public documentation. Private research notes live in `notes/`, which tracks `project/scriptmark` in `Acture/obsidian-vault`; start at `notes/README.md`. This checkout's root contains only this project's notes. Master places these notes under `scriptmark/`. Keep automation and vault configuration on master. Preserve existing local edits when updating a checkout.
-
-Install or refresh the trusted submission tools in Git metadata, including in new clones:
-
-```fish
-git -C notes fetch origin refs/heads/master:refs/remotes/origin/master
-set notes_common_gitdir (git -C notes rev-parse --path-format=absolute --git-common-dir)
-git -C notes show origin/master:.github/scripts/install_push_hook.py > "$notes_common_gitdir/install_push_hook.py"
-python3 "$notes_common_gitdir/install_push_hook.py" --repo notes --source-ref origin/master
-```
-
-After committing specific note files, submit through `python3 "$notes_common_gitdir/hooks/notes-boundary/submit_project.py" --repo notes`. The remote requires `notes-boundary/root/scriptmark` from GitHub Actions. Only after successful submission should this repository commit and push the `notes` gitlink. See the central repository's `项目接入.md` for initialization, updates and conflict handling.
diff --git a/Cargo.toml b/Cargo.toml
index ddac70d..9ca5f12 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -1,8 +1,8 @@
 [workspace]
 resolver = "2"
 members = [
-	"crates/scriptmark",
-	"crates/scriptmark-py",
+	"src/crates/scriptmark",
+	"src/crates/scriptmark-py",
 ]
 
 [workspace.package]
diff --git a/README.md b/README.md
index 51d4fc5..9f062f1 100644
--- a/README.md
+++ b/README.md
@@ -7,36 +7,62 @@
 
 Automated grading CLI for student programming assignments. Rust core, TOML test specifications, Python bindings via PyO3.
 
+## Repository layout
+
+```text
+src/
+  crates/
+    scriptmark/       Rust library, CLI and integration tests
+    scriptmark-py/    Rust bindings for the Python extension
+  python/
+    scriptmark/       Python package entry point
+examples/             Runnable teacher test bundles
+notes/                Private project documentation submodule
+```
+
+Run Cargo and Maturin commands from the repository root. `Cargo.toml` and
+`pyproject.toml` configure both builds; the compiled Python extension is packaged
+with `src/python/scriptmark/`.
+
 ## Documentation and checkout
 
-Project documentation lives in
+Public documentation belongs in `docs/`. Private project documentation lives in
 [Acture/obsidian-vault, branch `project/scriptmark`](https://github.com/Acture/obsidian-vault/tree/project/scriptmark),
 mounted here as the `notes/` submodule. Start with
-[the project index](https://github.com/Acture/obsidian-vault/blob/project/scriptmark/scriptmark/README.md)
+[the project index](https://github.com/Acture/obsidian-vault/blob/project/scriptmark/README.md)
 or open `notes/README.md` locally. The teacher guide is
 `notes/docs/test-bundles.md`; design records are under
 `notes/docs/plans/`. Access to the notes repository is required to initialize it.
+Building and using ScriptMark does not require access to private notes.
 
-Daily work uses the latest `project/scriptmark` notes. Clone, then initialize/update
-the notes and attach their project branch:
+Daily work uses the latest `project/scriptmark` notes through Git's native submodule
+commands. In a new clone, initialize the notes and attach their project branch:
 
 ```fish
 git clone https://github.com/Acture/scriptmark.git
-cd scriptmark
-fish scripts/update-notes.fish
+and cd scriptmark
+and git submodule update --init --remote --no-single-branch -- notes
+and git -C notes switch project/scriptmark
 ```
 
 At the start of each work session, after pulling code changes, and before reading or
-editing notes, use the same command:
+editing an existing notes checkout, update it from the project branch:
 
 ```fish
-fish scripts/update-notes.fish
+git -C notes -c fetch.prune=false -c fetch.pruneTags=false fetch --no-tags origin refs/heads/project/scriptmark:refs/remotes/origin/project/scriptmark
+and test (git -C notes status --porcelain | count) -eq 0
+and git -C notes merge-base --is-ancestor HEAD origin/project/scriptmark
+and git -C notes switch project/scriptmark
+and git -C notes merge-base --is-ancestor HEAD origin/project/scriptmark
+and git -C notes merge --ff-only origin/project/scriptmark
 ```
 
-The helper fetches the configured project branch, fast-forwards it and leaves it
-checked out for editing. It also works after a single-branch clone. Local edits,
-unpushed commits and divergence stop the update so they can be preserved and resolved.
-If fetching fails, the checkout has not been confirmed current.
+The explicit fetch also works with a single-branch notes clone. The checks before
+and after switching preserve unpublished work both at the current HEAD and on an
+existing local project branch. A failed command stops the sequence: inspect
+`git -C notes status` and `git -C notes log --oneline origin/project/scriptmark..HEAD`,
+then preserve and reconcile local edits, unpushed commits or divergence. Do not skip
+the checks or reset the notes. If fetching fails, the checkout is not confirmed current.
 
 Git still records a concrete submodule commit in each code commit. That is a saved
 checkpoint, not the daily reading policy; newer notes normally make `git status` show
@@ -49,20 +75,36 @@ git commit -m "docs: update ScriptMark notes"
 git push
 ```
 
-To edit documentation, update first, then publish the notes before the parent reference:
+Before the first documentation push in a clone, install the trusted boundary checker
+from the notes repository's `master`. Repeat this when its submission tooling changes:
+
+```fish
+git -C notes -c fetch.prune=false -c fetch.pruneTags=false fetch --no-tags origin refs/heads/master:refs/remotes/origin/master
+and set notes_common_gitdir (git -C notes rev-parse --path-format=absolute --git-common-dir)
+and git -C notes show origin/master:.github/scripts/install_push_hook.py > "$notes_common_gitdir/install_push_hook.py"
+and python3 "$notes_common_gitdir/install_push_hook.py" --repo notes --source-ref origin/master
+```
+
+To edit documentation, complete the update sequence above first, then publish the
+notes before the parent reference:
 
 ```fish
-fish scripts/update-notes.fish
-# Edit notes/; inspect the changes before staging.
-git -C notes diff -- scriptmark/
+# Edit project documents directly in notes/; stage the specific files changed.
+git -C notes diff
 git -C notes add README.md
 git -C notes commit -m "docs(scriptmark): describe the change"
-python3 (git -C notes rev-parse --path-format=absolute --git-common-dir)/hooks/notes-boundary/submit_project.py --repo notes
+set notes_common_gitdir (git -C notes rev-parse --path-format=absolute --git-common-dir)
+python3 "$notes_common_gitdir/hooks/notes-boundary/submit_project.py" --repo notes
 and git add notes
 and git commit -m "docs: update ScriptMark notes"
 and git push
 ```
 
+The submission helper runs the required remote boundary check and pushes the checked
+commit. A direct push of an unchecked commit is rejected. The notes repository's
+[project instructions](https://github.com/Acture/obsidian-vault/blob/master/项目接入.md)
+own this workflow.
+
 Push the notes successfully **before** updating the code repository's gitlink. If a
 fast-forward fails, resolve the divergence while preserving both versions. Do not
 force-push or discard notes. Runtime code, examples and artifacts stay in this repository;
@@ -71,7 +113,9 @@ documentation edits belong on the notes branch.
 Only when explicitly reproducing an older code revision, restore its recorded notes
 with `git submodule update --init --checkout -- notes` from a clean notes checkout.
 Ordinary `git clone --recurse-submodules` uses that recorded checkpoint too; run the
-helper afterwards for current notes. Git has no floating gitlink that advances by itself.
+update sequence above afterwards for current notes. Git has no floating gitlink that
+advances by itself. Shared notes tooling and its maintenance belong to the notes
+repository; ScriptMark does not carry its own synchronization script.
 
 ## Installation
 
@@ -199,7 +243,7 @@ print(spec.name, spec.function, spec.num_cases)
 Teachers can configure student ownership, item file patterns, function aliases and
 per-student overrides in `assignment.toml`. Preview decisions and candidates with
 `scriptmark match`; unresolved conflicts withhold grades. See
-[matching rules](https://github.com/Acture/obsidian-vault/blob/project/scriptmark/scriptmark/docs/matching.md).
+[matching rules](https://github.com/Acture/obsidian-vault/blob/project/scriptmark/docs/matching.md).
 
 ```toml
 [meta]
@@ -247,7 +291,7 @@ Reference answers are computed before grading and frozen for reuse. `--replay` v
 their sources and configuration, then reuses the answers without recomputing them.
 References can also supply declared exceptions, stdout and text files; see the
 [reference bundle](examples/bundles/reference_oracle) and
-[answer contract](https://github.com/Acture/obsidian-vault/blob/project/scriptmark/scriptmark/docs/test-bundles.md#reference-implementations).
+[answer contract](https://github.com/Acture/obsidian-vault/blob/project/scriptmark/docs/test-bundles.md#reference-implementations).
 
 Every case runs in its own process and working directory. When state should carry over —
 an object built once and driven step by step — say so with a scenario:
@@ -278,7 +322,7 @@ expect = 150
 Anything a bundle cannot honour — an unknown field, a checker that does not exist, a
 case with nothing to judge — is refused before a single student runs. Every failure says
 whose it is: the student's, the teacher's, or the machine's. See
-[the teacher guide](https://github.com/Acture/obsidian-vault/blob/project/scriptmark/scriptmark/docs/test-bundles.md) for the full contract, and
+[the teacher guide](https://github.com/Acture/obsidian-vault/blob/project/scriptmark/docs/test-bundles.md) for the full contract, and
 [examples/bundles](examples/bundles) for a pure function, a shared object and file I/O.
 
 ### Scoring
@@ -305,7 +349,7 @@ points = 3
 aggregation = "proportional"  # points × pass rate; or "all_or_nothing"
 ```
 
-See [the scoring contract](https://github.com/Acture/obsidian-vault/blob/project/scriptmark/scriptmark/docs/test-bundles.md#scoring) for every rule.
+See [the scoring contract](https://github.com/Acture/obsidian-vault/blob/project/scriptmark/docs/test-bundles.md#scoring) for every rule.
 
 ### Checkers
 
@@ -323,7 +367,7 @@ See [the scoring contract](https://github.com/Acture/obsidian-vault/blob/project
 ## Features
 
 - **Custom test engine** -- subprocess execution, no pytest dependency
-- **Isolated units** -- a process and directory per case, env isolation, import allowlist, setrlimit, timeout with kill; contains accidents, not a security sandbox ([details](https://github.com/Acture/obsidian-vault/blob/project/scriptmark/scriptmark/docs/test-bundles.md#what-grading-does-not-defend-against))
+- **Isolated units** -- a process and directory per case, env isolation, import allowlist, setrlimit, timeout with kill; contains accidents, not a security sandbox ([details](https://github.com/Acture/obsidian-vault/blob/project/scriptmark/docs/test-bundles.md#what-grading-does-not-defend-against))
 - **Parallel** -- tokio orchestrator, grades 80+ students in seconds
 - **Parametrize + oracle** -- random inputs with teacher reference implementations
 - **Per-item scoring** -- declared points and aggregation; zero and withheld kept apart in every export
diff --git a/pyproject.toml b/pyproject.toml
index 6e6f847..7d3f31e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -22,5 +22,5 @@ classifiers = [
 [tool.maturin]
 features = ["pyo3/extension-module"]
 module-name = "scriptmark._scriptmark"
-manifest-path = "crates/scriptmark-py/Cargo.toml"
-python-source = "python"
+manifest-path = "src/crates/scriptmark-py/Cargo.toml"
+python-source = "src/python"
diff --git a/scripts/update-notes.fish b/scripts/update-notes.fish
deleted file mode 100755
index b5f7b9e..0000000
--- a/scripts/update-notes.fish
+++ /dev/null
@@ -1,48 +0,0 @@
-#!/usr/bin/env fish
-
-# Daily notes follow the configured project branch; the gitlink is a saved checkpoint.
-set -l script_dir (status dirname)
-set -l repo_root (path resolve "$script_dir/..")
-set -l notes_path "$repo_root/notes"
-set -l branch (git -C "$repo_root" config -f .gitmodules --get submodule.notes.branch)
-or exit 1
-
-if not test -e "$notes_path/.git"
-	git -C "$repo_root" submodule sync -- notes
-	or exit 1
-	git -C "$repo_root" submodule update --init --remote --no-single-branch -- notes
-	or exit 1
-end
-
-set -l changes (git -C "$notes_path" status --porcelain)
-or exit 1
-if test (count $changes) -gt 0
-	printf '%s\n' 'Notes have local changes. Commit or preserve them before updating.' >&2
-	exit 1
-end
-
-# A single-branch clone may otherwise fetch only the vault's default branch.
-git -C "$notes_path" remote set-branches origin "$branch"
-or exit 1
-git -C "$notes_path" -c fetch.prune=false -c fetch.pruneTags=false fetch origin
-or exit 1
-
-if not git -C "$notes_path" merge-base --is-ancestor HEAD "origin/$branch"
-	printf '%s\n' "Notes HEAD has commits outside origin/$branch. Preserve and reconcile them before updating." >&2
-	exit 1
-end
-
-if git -C "$notes_path" show-ref --verify --quiet "refs/heads/$branch"
-	if not git -C "$notes_path" merge-base --is-ancestor "$branch" "origin/$branch"
-		printf '%s\n' "Local $branch has unpushed or divergent commits. Publish or reconcile them before updating." >&2
-		exit 1
-	end
-	git -C "$notes_path" switch "$branch"
-else
-	git -C "$notes_path" switch --create "$branch" --track "origin/$branch"
-end
-or exit 1
-
-git -C "$notes_path" merge --ff-only "origin/$branch"
-or exit 1
-printf 'Notes: %s @ %s\n' "$branch" (git -C "$notes_path" rev-parse --short HEAD)
diff --git a/crates/scriptmark-py/Cargo.toml b/src/crates/scriptmark-py/Cargo.toml
similarity index 100%
rename from crates/scriptmark-py/Cargo.toml
rename to src/crates/scriptmark-py/Cargo.toml
diff --git a/crates/scriptmark-py/src/lib.rs b/src/crates/scriptmark-py/src/lib.rs
similarity index 100%
rename from crates/scriptmark-py/src/lib.rs
rename to src/crates/scriptmark-py/src/lib.rs
diff --git a/crates/scriptmark/Cargo.toml b/src/crates/scriptmark/Cargo.toml
similarity index 97%
rename from crates/scriptmark/Cargo.toml
rename to src/crates/scriptmark/Cargo.toml
index 509bb03..6925fa5 100644
--- a/crates/scriptmark/Cargo.toml
+++ b/src/crates/scriptmark/Cargo.toml
@@ -9,7 +9,7 @@ repository.workspace = true
 homepage.workspace = true
 keywords.workspace = true
 categories.workspace = true
-readme = "../../README.md"
+readme = "../../../README.md"
 
 [[bin]]
 name = "scriptmark"
diff --git a/crates/scriptmark/src/archive.rs b/src/crates/scriptmark/src/archive.rs
similarity index 100%
rename from crates/scriptmark/src/archive.rs
rename to src/crates/scriptmark/src/archive.rs
diff --git a/crates/scriptmark/src/assignment.rs b/src/crates/scriptmark/src/assignment.rs
similarity index 100%
rename from crates/scriptmark/src/assignment.rs
rename to src/crates/scriptmark/src/assignment.rs
diff --git a/crates/scriptmark/src/canvas/bundle.rs b/src/crates/scriptmark/src/canvas/bundle.rs
similarity index 100%
rename from crates/scriptmark/src/canvas/bundle.rs
rename to src/crates/scriptmark/src/canvas/bundle.rs
diff --git a/crates/scriptmark/src/canvas/client.rs b/src/crates/scriptmark/src/canvas/client.rs
similarity index 100%
rename from crates/scriptmark/src/canvas/client.rs
rename to src/crates/scriptmark/src/canvas/client.rs
diff --git a/crates/scriptmark/src/canvas/mod.rs b/src/crates/scriptmark/src/canvas/mod.rs
similarity index 100%
rename from crates/scriptmark/src/canvas/mod.rs
rename to src/crates/scriptmark/src/canvas/mod.rs
diff --git a/crates/scriptmark/src/checker/builtin.rs b/src/crates/scriptmark/src/checker/builtin.rs
similarity index 100%
rename from crates/scriptmark/src/checker/builtin.rs
rename to src/crates/scriptmark/src/checker/builtin.rs
diff --git a/crates/scriptmark/src/checker/mod.rs b/src/crates/scriptmark/src/checker/mod.rs
similarity index 100%
rename from crates/scriptmark/src/checker/mod.rs
rename to src/crates/scriptmark/src/checker/mod.rs
diff --git a/crates/scriptmark/src/checker/python_checker.rs b/src/crates/scriptmark/src/checker/python_checker.rs
similarity index 100%
rename from crates/scriptmark/src/checker/python_checker.rs
rename to src/crates/scriptmark/src/checker/python_checker.rs
diff --git a/crates/scriptmark/src/checker/rhai_checker.rs b/src/crates/scriptmark/src/checker/rhai_checker.rs
similarity index 100%
rename from crates/scriptmark/src/checker/rhai_checker.rs
rename to src/crates/scriptmark/src/checker/rhai_checker.rs
diff --git a/crates/scriptmark/src/db/mod.rs b/src/crates/scriptmark/src/db/mod.rs
similarity index 100%
rename from crates/scriptmark/src/db/mod.rs
rename to src/crates/scriptmark/src/db/mod.rs
diff --git a/crates/scriptmark/src/db/queries.rs b/src/crates/scriptmark/src/db/queries.rs
similarity index 100%
rename from crates/scriptmark/src/db/queries.rs
rename to src/crates/scriptmark/src/db/queries.rs
diff --git a/crates/scriptmark/src/db/results.rs b/src/crates/scriptmark/src/db/results.rs
similarity index 100%
rename from crates/scriptmark/src/db/results.rs
rename to src/crates/scriptmark/src/db/results.rs
diff --git a/crates/scriptmark/src/db/roster.rs b/src/crates/scriptmark/src/db/roster.rs
similarity index 100%
rename from crates/scriptmark/src/db/roster.rs
rename to src/crates/scriptmark/src/db/roster.rs
diff --git a/crates/scriptmark/src/db/schema.rs b/src/crates/scriptmark/src/db/schema.rs
similarity index 100%
rename from crates/scriptmark/src/db/schema.rs
rename to src/crates/scriptmark/src/db/schema.rs
diff --git a/crates/scriptmark/src/discovery.rs b/src/crates/scriptmark/src/discovery.rs
similarity index 100%
rename from crates/scriptmark/src/discovery.rs
rename to src/crates/scriptmark/src/discovery.rs
diff --git a/crates/scriptmark/src/display.rs b/src/crates/scriptmark/src/display.rs
similarity index 100%
rename from crates/scriptmark/src/display.rs
rename to src/crates/scriptmark/src/display.rs
diff --git a/crates/scriptmark/src/export.rs b/src/crates/scriptmark/src/export.rs
similarity index 100%
rename from crates/scriptmark/src/export.rs
rename to src/crates/scriptmark/src/export.rs
diff --git a/crates/scriptmark/src/grading.rs b/src/crates/scriptmark/src/grading.rs
similarity index 100%
rename from crates/scriptmark/src/grading.rs
rename to src/crates/scriptmark/src/grading.rs
diff --git a/crates/scriptmark/src/input/canvas.rs b/src/crates/scriptmark/src/input/canvas.rs
similarity index 100%
rename from crates/scriptmark/src/input/canvas.rs
rename to src/crates/scriptmark/src/input/canvas.rs
diff --git a/crates/scriptmark/src/input/mod.rs b/src/crates/scriptmark/src/input/mod.rs
similarity index 100%
rename from crates/scriptmark/src/input/mod.rs
rename to src/crates/scriptmark/src/input/mod.rs
diff --git a/crates/scriptmark/src/lib.rs b/src/crates/scriptmark/src/lib.rs
similarity index 100%
rename from crates/scriptmark/src/lib.rs
rename to src/crates/scriptmark/src/lib.rs
diff --git a/crates/scriptmark/src/main.rs b/src/crates/scriptmark/src/main.rs
similarity index 100%
rename from crates/scriptmark/src/main.rs
rename to src/crates/scriptmark/src/main.rs
diff --git a/crates/scriptmark/src/matching.py b/src/crates/scriptmark/src/matching.py
similarity index 100%
rename from crates/scriptmark/src/matching.py
rename to src/crates/scriptmark/src/matching.py
diff --git a/crates/scriptmark/src/matching.rs b/src/crates/scriptmark/src/matching.rs
similarity index 100%
rename from crates/scriptmark/src/matching.rs
rename to src/crates/scriptmark/src/matching.rs
diff --git a/crates/scriptmark/src/models/config.rs b/src/crates/scriptmark/src/models/config.rs
similarity index 100%
rename from crates/scriptmark/src/models/config.rs
rename to src/crates/scriptmark/src/models/config.rs
diff --git a/crates/scriptmark/src/models/mod.rs b/src/crates/scriptmark/src/models/mod.rs
similarity index 100%
rename from crates/scriptmark/src/models/mod.rs
rename to src/crates/scriptmark/src/models/mod.rs
diff --git a/crates/scriptmark/src/models/result.rs b/src/crates/scriptmark/src/models/result.rs
similarity index 100%
rename from crates/scriptmark/src/models/result.rs
rename to src/crates/scriptmark/src/models/result.rs
diff --git a/crates/scriptmark/src/models/spec.rs b/src/crates/scriptmark/src/models/spec.rs
similarity index 100%
rename from crates/scriptmark/src/models/spec.rs
rename to src/crates/scriptmark/src/models/spec.rs
diff --git a/crates/scriptmark/src/models/submission.rs b/src/crates/scriptmark/src/models/submission.rs
similarity index 100%
rename from crates/scriptmark/src/models/submission.rs
rename to src/crates/scriptmark/src/models/submission.rs
diff --git a/crates/scriptmark/src/record.rs b/src/crates/scriptmark/src/record.rs
similarity index 100%
rename from crates/scriptmark/src/record.rs
rename to src/crates/scriptmark/src/record.rs
diff --git a/crates/scriptmark/src/report.rs b/src/crates/scriptmark/src/report.rs
similarity index 100%
rename from crates/scriptmark/src/report.rs
rename to src/crates/scriptmark/src/report.rs
diff --git a/crates/scriptmark/src/report_template.html b/src/crates/scriptmark/src/report_template.html
similarity index 100%
rename from crates/scriptmark/src/report_template.html
rename to src/crates/scriptmark/src/report_template.html
diff --git a/crates/scriptmark/src/roster.rs b/src/crates/scriptmark/src/roster.rs
similarity index 100%
rename from crates/scriptmark/src/roster.rs
rename to src/crates/scriptmark/src/roster.rs
diff --git a/crates/scriptmark/src/runner/answers.rs b/src/crates/scriptmark/src/runner/answers.rs
similarity index 100%
rename from crates/scriptmark/src/runner/answers.rs
rename to src/crates/scriptmark/src/runner/answers.rs
diff --git a/crates/scriptmark/src/runner/executor.rs b/src/crates/scriptmark/src/runner/executor.rs
similarity index 100%
rename from crates/scriptmark/src/runner/executor.rs
rename to src/crates/scriptmark/src/runner/executor.rs
diff --git a/crates/scriptmark/src/runner/frozen.rs b/src/crates/scriptmark/src/runner/frozen.rs
similarity index 100%
rename from crates/scriptmark/src/runner/frozen.rs
rename to src/crates/scriptmark/src/runner/frozen.rs
diff --git a/crates/scriptmark/src/runner/generation.rs b/src/crates/scriptmark/src/runner/generation.rs
similarity index 100%
rename from crates/scriptmark/src/runner/generation.rs
rename to src/crates/scriptmark/src/runner/generation.rs
diff --git a/crates/scriptmark/src/runner/generator.rs b/src/crates/scriptmark/src/runner/generator.rs
similarity index 100%
rename from crates/scriptmark/src/runner/generator.rs
rename to src/crates/scriptmark/src/runner/generator.rs
diff --git a/crates/scriptmark/src/runner/harness.py b/src/crates/scriptmark/src/runner/harness.py
similarity index 99%
rename from crates/scriptmark/src/runner/harness.py
rename to src/crates/scriptmark/src/runner/harness.py
index 6910f21..4b4e223 100644
--- a/crates/scriptmark/src/runner/harness.py
+++ b/src/crates/scriptmark/src/runner/harness.py
@@ -355,7 +355,7 @@ def _removed_checker(*args, **kwargs):
 		"@checker no longer binds a checker to a function: put "
 		'check = { function = "<checker name>" } on each case it should judge '
 		"(https://github.com/Acture/obsidian-vault/blob/project/scriptmark/"
-		"scriptmark/docs/test-bundles.md#migrating-an-older-spec)"
+		"docs/test-bundles.md#migrating-an-older-spec)"
 	)
 
 
diff --git a/crates/scriptmark/src/runner/judge.rs b/src/crates/scriptmark/src/runner/judge.rs
similarity index 100%
rename from crates/scriptmark/src/runner/judge.rs
rename to src/crates/scriptmark/src/runner/judge.rs
diff --git a/crates/scriptmark/src/runner/linter.rs b/src/crates/scriptmark/src/runner/linter.rs
similarity index 100%
rename from crates/scriptmark/src/runner/linter.rs
rename to src/crates/scriptmark/src/runner/linter.rs
diff --git a/crates/scriptmark/src/runner/mod.rs b/src/crates/scriptmark/src/runner/mod.rs
similarity index 100%
rename from crates/scriptmark/src/runner/mod.rs
rename to src/crates/scriptmark/src/runner/mod.rs
diff --git a/crates/scriptmark/src/runner/oracle.rs b/src/crates/scriptmark/src/runner/oracle.rs
similarity index 100%
rename from crates/scriptmark/src/runner/oracle.rs
rename to src/crates/scriptmark/src/runner/oracle.rs
diff --git a/crates/scriptmark/src/runner/orchestrator.rs b/src/crates/scriptmark/src/runner/orchestrator.rs
similarity index 100%
rename from crates/scriptmark/src/runner/orchestrator.rs
rename to src/crates/scriptmark/src/runner/orchestrator.rs
diff --git a/crates/scriptmark/src/runner/prepare.rs b/src/crates/scriptmark/src/runner/prepare.rs
similarity index 100%
rename from crates/scriptmark/src/runner/prepare.rs
rename to src/crates/scriptmark/src/runner/prepare.rs
diff --git a/crates/scriptmark/src/runner/python.rs b/src/crates/scriptmark/src/runner/python.rs
similarity index 100%
rename from crates/scriptmark/src/runner/python.rs
rename to src/crates/scriptmark/src/runner/python.rs
diff --git a/crates/scriptmark/src/runner/records.rs b/src/crates/scriptmark/src/runner/records.rs
similarity index 100%
rename from crates/scriptmark/src/runner/records.rs
rename to src/crates/scriptmark/src/runner/records.rs
diff --git a/crates/scriptmark/src/runner/sandbox.rs b/src/crates/scriptmark/src/runner/sandbox.rs
similarity index 100%
rename from crates/scriptmark/src/runner/sandbox.rs
rename to src/crates/scriptmark/src/runner/sandbox.rs
diff --git a/crates/scriptmark/src/similarity.rs b/src/crates/scriptmark/src/similarity.rs
similarity index 100%
rename from crates/scriptmark/src/similarity.rs
rename to src/crates/scriptmark/src/similarity.rs
diff --git a/crates/scriptmark/src/spec_loader.rs b/src/crates/scriptmark/src/spec_loader.rs
similarity index 100%
rename from crates/scriptmark/src/spec_loader.rs
rename to src/crates/scriptmark/src/spec_loader.rs
diff --git a/crates/scriptmark/src/tui/app.rs b/src/crates/scriptmark/src/tui/app.rs
similarity index 100%
rename from crates/scriptmark/src/tui/app.rs
rename to src/crates/scriptmark/src/tui/app.rs
diff --git a/crates/scriptmark/src/tui/mod.rs b/src/crates/scriptmark/src/tui/mod.rs
similarity index 100%
rename from crates/scriptmark/src/tui/mod.rs
rename to src/crates/scriptmark/src/tui/mod.rs
diff --git a/crates/scriptmark/src/tui/ui.rs b/src/crates/scriptmark/src/tui/ui.rs
similarity index 100%
rename from crates/scriptmark/src/tui/ui.rs
rename to src/crates/scriptmark/src/tui/ui.rs
diff --git a/crates/scriptmark/tests/canvas_fetch.rs b/src/crates/scriptmark/tests/canvas_fetch.rs
similarity index 100%
rename from crates/scriptmark/tests/canvas_fetch.rs
rename to src/crates/scriptmark/tests/canvas_fetch.rs
diff --git a/crates/scriptmark/tests/cli.rs b/src/crates/scriptmark/tests/cli.rs
similarity index 100%
rename from crates/scriptmark/tests/cli.rs
rename to src/crates/scriptmark/tests/cli.rs
diff --git a/crates/scriptmark/tests/examples.rs b/src/crates/scriptmark/tests/examples.rs
similarity index 99%
rename from crates/scriptmark/tests/examples.rs
rename to src/crates/scriptmark/tests/examples.rs
index 32a1a42..4d4ffcc 100644
--- a/crates/scriptmark/tests/examples.rs
+++ b/src/crates/scriptmark/tests/examples.rs
@@ -17,7 +17,7 @@ use scriptmark::runner::python::PythonExecutor;
 use scriptmark::spec_loader::{load_spec, load_specs_from_dir};
 
 fn examples() -> PathBuf {
-	Path::new(env!("CARGO_MANIFEST_DIR")).join("../../examples")
+	Path::new(env!("CARGO_MANIFEST_DIR")).join("../../../examples")
 }
 
 async fn grade_example(name: &str) -> Vec<StudentReport> {
diff --git a/crates/scriptmark/tests/fixtures/archives/m3_default.rar b/src/crates/scriptmark/tests/fixtures/archives/m3_default.rar
similarity index 100%
rename from crates/scriptmark/tests/fixtures/archives/m3_default.rar
rename to src/crates/scriptmark/tests/fixtures/archives/m3_default.rar
diff --git a/crates/scriptmark/tests/fixtures/hw1/canvas/assignment.json b/src/crates/scriptmark/tests/fixtures/hw1/canvas/assignment.json
similarity index 100%
rename from crates/scriptmark/tests/fixtures/hw1/canvas/assignment.json
rename to src/crates/scriptmark/tests/fixtures/hw1/canvas/assignment.json
diff --git a/crates/scriptmark/tests/fixtures/hw1/canvas/files/1001/lab1.py b/src/crates/scriptmark/tests/fixtures/hw1/canvas/files/1001/lab1.py
similarity index 100%
rename from crates/scriptmark/tests/fixtures/hw1/canvas/files/1001/lab1.py
rename to src/crates/scriptmark/tests/fixtures/hw1/canvas/files/1001/lab1.py
diff --git a/crates/scriptmark/tests/fixtures/hw1/canvas/files/1002/draft.py b/src/crates/scriptmark/tests/fixtures/hw1/canvas/files/1002/draft.py
similarity index 100%
rename from crates/scriptmark/tests/fixtures/hw1/canvas/files/1002/draft.py
rename to src/crates/scriptmark/tests/fixtures/hw1/canvas/files/1002/draft.py
diff --git a/crates/scriptmark/tests/fixtures/hw1/canvas/files/1003/lab1.py b/src/crates/scriptmark/tests/fixtures/hw1/canvas/files/1003/lab1.py
similarity index 100%
rename from crates/scriptmark/tests/fixtures/hw1/canvas/files/1003/lab1.py
rename to src/crates/scriptmark/tests/fixtures/hw1/canvas/files/1003/lab1.py
diff --git a/crates/scriptmark/tests/fixtures/hw1/canvas/files/1004/lab1.py b/src/crates/scriptmark/tests/fixtures/hw1/canvas/files/1004/lab1.py
similarity index 100%
rename from crates/scriptmark/tests/fixtures/hw1/canvas/files/1004/lab1.py
rename to src/crates/scriptmark/tests/fixtures/hw1/canvas/files/1004/lab1.py
diff --git a/crates/scriptmark/tests/fixtures/hw1/canvas/files/1005/lab1.py b/src/crates/scriptmark/tests/fixtures/hw1/canvas/files/1005/lab1.py
similarity index 100%
rename from crates/scriptmark/tests/fixtures/hw1/canvas/files/1005/lab1.py
rename to src/crates/scriptmark/tests/fixtures/hw1/canvas/files/1005/lab1.py
diff --git a/crates/scriptmark/tests/fixtures/hw1/legacy_results.json b/src/crates/scriptmark/tests/fixtures/hw1/legacy_results.json
similarity index 100%
rename from crates/scriptmark/tests/fixtures/hw1/legacy_results.json
rename to src/crates/scriptmark/tests/fixtures/hw1/legacy_results.json
diff --git a/crates/scriptmark/tests/fixtures/hw1/local/roster.csv b/src/crates/scriptmark/tests/fixtures/hw1/local/roster.csv
similarity index 100%
rename from crates/scriptmark/tests/fixtures/hw1/local/roster.csv
rename to src/crates/scriptmark/tests/fixtures/hw1/local/roster.csv
diff --git a/crates/scriptmark/tests/fixtures/hw1/local/submissions/0024010003_lab1.py b/src/crates/scriptmark/tests/fixtures/hw1/local/submissions/0024010003_lab1.py
similarity index 100%
rename from crates/scriptmark/tests/fixtures/hw1/local/submissions/0024010003_lab1.py
rename to src/crates/scriptmark/tests/fixtures/hw1/local/submissions/0024010003_lab1.py
diff --git a/crates/scriptmark/tests/fixtures/hw1/local/submissions/2024010001_lab1.py b/src/crates/scriptmark/tests/fixtures/hw1/local/submissions/2024010001_lab1.py
similarity index 100%
rename from crates/scriptmark/tests/fixtures/hw1/local/submissions/2024010001_lab1.py
rename to src/crates/scriptmark/tests/fixtures/hw1/local/submissions/2024010001_lab1.py
diff --git a/crates/scriptmark/tests/fixtures/hw1/local/submissions/2024010002_lab1.py b/src/crates/scriptmark/tests/fixtures/hw1/local/submissions/2024010002_lab1.py
similarity index 100%
rename from crates/scriptmark/tests/fixtures/hw1/local/submissions/2024010002_lab1.py
rename to src/crates/scriptmark/tests/fixtures/hw1/local/submissions/2024010002_lab1.py
diff --git a/crates/scriptmark/tests/fixtures/hw1/local/submissions/2024010005_notes.txt b/src/crates/scriptmark/tests/fixtures/hw1/local/submissions/2024010005_notes.txt
similarity index 100%
rename from crates/scriptmark/tests/fixtures/hw1/local/submissions/2024010005_notes.txt
rename to src/crates/scriptmark/tests/fixtures/hw1/local/submissions/2024010005_notes.txt
diff --git a/crates/scriptmark/tests/fixtures/hw1/local/submissions/24010003_lab1.py b/src/crates/scriptmark/tests/fixtures/hw1/local/submissions/24010003_lab1.py
similarity index 100%
rename from crates/scriptmark/tests/fixtures/hw1/local/submissions/24010003_lab1.py
rename to src/crates/scriptmark/tests/fixtures/hw1/local/submissions/24010003_lab1.py
diff --git a/crates/scriptmark/tests/fixtures/hw1/local/submissions/_scratch_v2.py b/src/crates/scriptmark/tests/fixtures/hw1/local/submissions/_scratch_v2.py
similarity index 100%
rename from crates/scriptmark/tests/fixtures/hw1/local/submissions/_scratch_v2.py
rename to src/crates/scriptmark/tests/fixtures/hw1/local/submissions/_scratch_v2.py
diff --git a/crates/scriptmark/tests/generated.rs b/src/crates/scriptmark/tests/generated.rs
similarity index 100%
rename from crates/scriptmark/tests/generated.rs
rename to src/crates/scriptmark/tests/generated.rs
diff --git a/crates/scriptmark/tests/harness.rs b/src/crates/scriptmark/tests/harness.rs
similarity index 100%
rename from crates/scriptmark/tests/harness.rs
rename to src/crates/scriptmark/tests/harness.rs
diff --git a/crates/scriptmark/tests/input_equivalence.rs b/src/crates/scriptmark/tests/input_equivalence.rs
similarity index 100%
rename from crates/scriptmark/tests/input_equivalence.rs
rename to src/crates/scriptmark/tests/input_equivalence.rs
diff --git a/crates/scriptmark/tests/integration.rs b/src/crates/scriptmark/tests/integration.rs
similarity index 100%
rename from crates/scriptmark/tests/integration.rs
rename to src/crates/scriptmark/tests/integration.rs
diff --git a/crates/scriptmark/tests/matching.rs b/src/crates/scriptmark/tests/matching.rs
similarity index 100%
rename from crates/scriptmark/tests/matching.rs
rename to src/crates/scriptmark/tests/matching.rs
diff --git a/crates/scriptmark/tests/oracle.rs b/src/crates/scriptmark/tests/oracle.rs
similarity index 100%
rename from crates/scriptmark/tests/oracle.rs
rename to src/crates/scriptmark/tests/oracle.rs
diff --git a/crates/scriptmark/tests/record.rs b/src/crates/scriptmark/tests/record.rs
similarity index 100%
rename from crates/scriptmark/tests/record.rs
rename to src/crates/scriptmark/tests/record.rs
diff --git a/python/scriptmark/__init__.py b/src/python/scriptmark/__init__.py
similarity index 100%
rename from python/scriptmark/__init__.py
rename to src/python/scriptmark/__init__.py