feat(completion): 自动安装 shell 补全，迁移旧配置并清理手动补全

.claude/skills/mytoolkit/SKILL.md

@@ -25,10 +25,11 @@ triggers:
 
 # MyToolkit 个人 CLI 工具集
 
-`mytoolkit` 是日常文件处理、格式转换、批量操作的便捷工具集。所有命令统一在 `mytoolkit` 命名空间下，支持 zsh tab completion。
+`mytoolkit` 是日常文件处理、格式转换、批量操作的便捷工具集。所有命令统一在 `mytoolkit` 命名空间下，支持 zsh/bash tab completion。补全脚本由 `mytoolkit completion install` 自动安装到当前 Python prefix，首次运行任意命令时若缺失会自动补齐。
 
 ```bash
-eval "$(_MYTOOLKIT_COMPLETE=zsh_source mytoolkit)"
+mytoolkit completion doctor    # 检查补全安装状态
+mytoolkit completion zsh       # 打印 zsh 补全脚本
 ```
 
 ## 与其他 Skill 的分工
@@ -54,7 +55,7 @@ eval "$(_MYTOOLKIT_COMPLETE=zsh_source mytoolkit)"
 | `video` | 视频格式转换 | `references/video.md` |
 | `webpage` | Docusaurus 网站构建、部署、server 管理 | `mytoolkit info docs webpage` |
 | `mail` | 邮箱管理（inbox、read、draft） | `references/mail.md` |
-| `env/git/ssh/server/update/uninstall` | 其他辅助命令 | `references/others.md` |
+| `env/git/ssh/server/update/uninstall/completion` | 其他辅助命令 | `references/others.md` |
 
 > 注：`convert`、`pdf`、`webpage` 的完整参考文档已随 mytoolkit 包安装，通过 `mytoolkit info docs <name>` 直接读取；技能内 `references/` 仅保留速查。
 

.claude/skills/mytoolkit/references/others.md

@@ -10,4 +10,5 @@ mytoolkit ssh              # SSH 快捷连接
 mytoolkit server           # 开发服务器管理
 mytoolkit update           # 从本地仓库更新
 mytoolkit uninstall        # 卸载
+mytoolkit completion       # 安装/查看/卸载 shell 补全（install / uninstall / doctor / zsh / bash）
 ```

CLAUDE.md

@@ -78,7 +78,7 @@ mytoolkit voice tts "文本" -v zh_male_wennuanahu_moon_bigtts --format mp3 --sp
 mytoolkit init paper <dir>        # 默认 Elsevier elsarticle 模板（全平台可移植）
 ```
 
-生成 `main.tex`/`Makefile`/`diffpreamble.dtx`/`references.bib`/`figs/`/`analysis/`。**精确配置（文档类选项、字号、字体、书签层级）以脚手架 `main.tex` 头部注释为准，本文档不复述以免漂移。**
+生成 `main.tex`/`Makefile`/`diffpreamble.dtx`/`references.bib`/`figs/`。**精确配置（文档类选项、字号、字体、书签层级）以脚手架 `main.tex` 头部注释为准，本文档不复述以免漂移。**
 
 改脚手架时须保持的**设计约束**：
 - 文档类 **elsarticle**；正文+数学只用 **TeX Live 自带字体**（当前 Libertinus），**禁止写死系统/专有字体（如 Cambria）**，否则破坏可移植性；

Makefile

@@ -1,10 +1,6 @@
 ROOT_DIR := $(shell pwd)
-COMP_DIR := $(HOME)/.local/bin/completions
 PYTHON ?= python3
 
-# 手动安装的文件清单（与 bin/commands/self_mgmt.py 中的 _MANUAL_FILES 保持同步）
-MANUAL_FILES := $(COMP_DIR)/_mytoolkit $(COMP_DIR)/mytoolkit.bash
-
 .PHONY: help install uninstall sync-skill
 
 help:
@@ -12,22 +8,12 @@ help:
 	@echo ""
 	@echo "  install     Install mytoolkit in editable mode (current Python) and sync skill"
 	@echo "  sync-skill  Copy the bundled Claude skill to ~/.claude/skills/mytoolkit/"
-	@echo "  uninstall   Uninstall mytoolkit and remove completions"
+	@echo "  uninstall   Uninstall mytoolkit and remove shell completions"
 
 install:
 	$(PYTHON) -m pip install -e "$(ROOT_DIR)" --upgrade
-	@echo "Installing completions…"
-	@mkdir -p "$(COMP_DIR)"
-	@SHELL_NAME=$$(basename "$$SHELL"); \
-	if [ "$$SHELL_NAME" = "zsh" ]; then \
-		_MYTOOLKIT_COMPLETE=zsh_source mytoolkit > "$(COMP_DIR)/_mytoolkit" && \
-			echo "zsh completion: $(COMP_DIR)/_mytoolkit" || \
-			echo "Warning: zsh completion failed"; \
-	elif [ "$$SHELL_NAME" = "bash" ]; then \
-		_MYTOOLKIT_COMPLETE=bash_source mytoolkit > "$(COMP_DIR)/mytoolkit.bash" && \
-			echo "bash completion: $(COMP_DIR)/mytoolkit.bash" || \
-			echo "Warning: bash completion failed"; \
-	fi
+	@echo "Installing shell completions…"
+	@mytoolkit completion install || echo "Warning: completion install failed"
 	@$(MAKE) -s sync-skill
 
 sync-skill:
@@ -41,11 +27,4 @@ sync-skill:
 	fi
 
 uninstall:
-	$(PYTHON) -m pip uninstall mytoolkit -y
-	@for f in $(MANUAL_FILES); do \
-		if [ -e "$$f" ] || [ -L "$$f" ]; then \
-			rm -f "$$f"; \
-			echo "Removed $$f"; \
-		fi; \
-	done
-	@echo "Uninstalled mytoolkit and cleaned up manual files"
+	@mytoolkit uninstall || $(PYTHON) -m pip uninstall mytoolkit -y

README.md

@@ -12,9 +12,17 @@ mytoolkit templates list                      # verify bundled templates are fou
 
 `make install` 会同时：
 1. 用 editable 模式安装 `mytoolkit`；
-2. 生成 zsh/bash 补全；
+2. 自动安装 zsh/bash 补全到当前 Python prefix 的共享目录；
 3. 把 bundled Claude skill 同步到 `~/.claude/skills/mytoolkit/`。
 
+补全由 `mytoolkit` 自己管理，无需手动写 `~/.local/bin/completions`，也无需在 `.zshrc` 里 `eval`。首次运行任意 `mytoolkit` 命令时会自动补齐；也可以手动检查状态：
+
+```bash
+mytoolkit completion doctor
+mytoolkit completion install   # 手动重装补全
+mytoolkit completion zsh       # 打印 zsh 补全脚本
+```
+
 单独同步 skill（不重装 Python 包）：
 
 ```bash
@@ -58,6 +66,7 @@ mytoolkit --help
 | `server` | Manage dev/serve servers |
 | `update` | Reinstall from local repo |
 | `uninstall` | Uninstall |
+| `completion` | Install/inspect shell tab-completion scripts (`install` / `uninstall` / `doctor` / `zsh` / `bash`) |
 
 For any subcommand: `mytoolkit <cmd> --help`.
 
@@ -85,7 +94,7 @@ Registry is stored at `~/.mytoolkit/templates.json` (or `$MYTOOLKIT_HOME/templat
 mytoolkit init paper <dir>     # create a LaTeX paper project (Elsevier elsarticle, xelatex, fully portable)
 ```
 
-This generates `main.tex`, `Makefile`, `references.bib`, `diffpreamble.dtx`, `figs/`, `analysis/`.
+This generates `main.tex`, `Makefile`, `references.bib`, `diffpreamble.dtx`, `figs/`.
 
 ### Journal submission kits
 

mytoolkit/cli.py

@@ -16,6 +16,8 @@ from mytoolkit.commands.server import server_cmd
 from mytoolkit.commands.webpage import webpage_cmd
 from mytoolkit.commands.mycv import mycv_cmd
 from mytoolkit.commands.mail import mail
+from mytoolkit.commands.completion import build_completion_group
+from mytoolkit.commands.completion_install import ensure_completions_installed
 from mytoolkit.commands.self_mgmt import update_cmd, uninstall_cmd
 
 
@@ -47,10 +49,16 @@ cli.add_command(mycv_cmd)
 cli.add_command(mail)
 cli.add_command(update_cmd)
 cli.add_command(uninstall_cmd)
+cli.add_command(build_completion_group(lambda: cli))
 
 
 def main():
-    cli()
+    import sys
+
+    argv = sys.argv[1:]
+    if not argv or argv[0] != "completion":
+        ensure_completions_installed(cli)
+    cli.main(args=argv, prog_name="mytoolkit", standalone_mode=True)
 
 
 if __name__ == "__main__":

mytoolkit/commands/completion.py

@@ -0,0 +1,139 @@
+"""Shell tab-completion CLI for mytoolkit."""
+
+from __future__ import annotations
+
+import shlex
+import subprocess
+import sys
+from typing import TYPE_CHECKING
+
+import click
+from click.shell_completion import get_completion_class
+
+from mytoolkit.commands.completion_install import (
+    CLICK_COMPLETE_VAR,
+    PROG_NAME,
+    completion_targets,
+    completions_installed,
+    install_completions,
+    python_prefix,
+    python_share_dir,
+    uninstall_completions,
+)
+
+if TYPE_CHECKING:
+    from click.shell_completion import CompletionItem
+
+
+def _completion_script(cli: click.Command, shell: str) -> str:
+    shell_class = get_completion_class(shell)
+    if shell_class is None:
+        raise ValueError(f"unsupported shell for completion: {shell}")
+    comp = shell_class(cli, {}, PROG_NAME, CLICK_COMPLETE_VAR)
+    script = comp.source()
+    if not script.endswith("\n"):
+        script += "\n"
+    return script
+
+
+def _smoke_subcommands(cli: click.Command) -> list[str]:
+    shell_class = get_completion_class("bash")
+    if shell_class is None:
+        return []
+    comp = shell_class(cli, {}, PROG_NAME, CLICK_COMPLETE_VAR)
+    items: list[CompletionItem] = comp.get_completions([], "")
+    return sorted({item.value for item in items})
+
+
+def run_completion_doctor(cli: click.Command) -> None:
+    prefix = python_prefix()
+    share = python_share_dir()
+    click.echo(click.style("Python prefix", bold=True) + f": {prefix}")
+    click.echo(click.style("Share dir", bold=True) + f": {share}")
+    click.echo()
+
+    click.echo(click.style("Completion scripts", fg="blue", bold=True))
+    for target in completion_targets():
+        if target.installed and CLICK_COMPLETE_VAR in target.path.read_text(encoding="utf-8"):
+            status = click.style("ok", fg="green")
+        elif target.installed:
+            status = click.style("stale", fg="yellow")
+        else:
+            status = click.style("missing", fg="red")
+        click.echo(f"  {target.shell:5}  {target.path}  [{status}]")
+    click.echo()
+
+    zsh_dir = share / "zsh" / "site-functions"
+    if zsh_dir.is_dir():
+        try:
+            quoted = shlex.quote(str(zsh_dir))
+            check = subprocess.run(
+                [
+                    "zsh",
+                    "-c",
+                    f"source ~/.zshrc >/dev/null 2>&1; "
+                    f"[[ -n ${{fpath[(r){quoted}]}} ]] && echo yes",
+                ],
+                capture_output=True,
+                text=True,
+                check=False,
+            )
+            in_fpath = "yes" in check.stdout
+        except (OSError, subprocess.SubprocessError):
+            in_fpath = True  # be permissive if we cannot check
+        if not in_fpath:
+            click.echo(
+                click.style("Zsh", fg="yellow", bold=True)
+                + f": add to fpath if Tab does not work:\n  fpath=({zsh_dir} $fpath)"
+            )
+            click.echo()
+
+    if not completions_installed():
+        click.echo(
+            click.style("Fix", fg="yellow", bold=True)
+            + ": run `mytoolkit completion install` or reinstall the package."
+        )
+        return
+
+    subs = _smoke_subcommands(cli)
+    click.echo(
+        click.style("Smoke (subcommands)", fg="blue", bold=True) + f": {', '.join(subs)}"
+    )
+
+
+def build_completion_group(cli_factory):
+    @click.group(name="completion", help="Install or inspect shell tab-completion scripts.")
+    def completion() -> None:
+        pass
+
+    @completion.command("install")
+    def install_cmd() -> None:
+        """Write completion scripts under the active Python prefix."""
+        installed = install_completions(cli_factory())
+        if not installed:
+            raise click.ClickException("No completion files were written (prefix not writable?).")
+        for path in installed:
+            click.echo(path)
+
+    @completion.command("uninstall")
+    def uninstall_cmd() -> None:
+        """Remove completion scripts installed by this package."""
+        removed = uninstall_completions()
+        for path in removed:
+            click.echo(path)
+        if not removed:
+            click.echo("(nothing to remove)")
+
+    @completion.command("doctor")
+    def doctor_cmd() -> None:
+        """Report completion install state and run smoke checks."""
+        run_completion_doctor(cli_factory())
+
+    for shell in ("bash", "zsh"):
+
+        @completion.command(name=shell, help=f"Print the {shell} completion script to stdout.")
+        def print_shell(shell_name: str = shell) -> None:
+            script = _completion_script(cli_factory(), shell_name)
+            sys.stdout.write(script)
+
+    return completion

mytoolkit/commands/completion_install.py

@@ -0,0 +1,258 @@
+"""Install shell tab-completion files under the active Python prefix.
+
+Adapted from phynexis-server's completion_install.py to work with the
+mytoolkit Click CLI and hatchling-based editable installs.
+"""
+
+from __future__ import annotations
+
+import base64
+import hashlib
+import os
+import site
+import sysconfig
+from dataclasses import dataclass
+from pathlib import Path
+
+CLICK_COMPLETE_VAR = "_MYTOOLKIT_COMPLETE"
+PROG_NAME = "mytoolkit"
+MANIFEST_FILENAME = "completion-paths.txt"
+
+
+@dataclass(frozen=True)
+class _CompletionConfig:
+    zsh_filename: str
+    bash_filename: str
+    click_complete_var: str
+    dist_info_globs: tuple[str, ...]
+
+
+_CONFIG = _CompletionConfig(
+    zsh_filename="_mytoolkit",
+    bash_filename="mytoolkit",
+    click_complete_var=CLICK_COMPLETE_VAR,
+    dist_info_globs=("mytoolkit-*.dist-info",),
+)
+
+ZSH_FILENAME = _CONFIG.zsh_filename
+BASH_FILENAME = _CONFIG.bash_filename
+
+
+@dataclass(frozen=True)
+class CompletionTarget:
+    shell: str
+    path: Path
+
+    @property
+    def installed(self) -> bool:
+        return self.path.is_file()
+
+
+def python_share_dir(*, install_root: Path | None = None) -> Path:
+    if install_root is not None:
+        return install_root / "share"
+    data = Path(sysconfig.get_path("data"))
+    if data.name == "share":
+        return data
+    return data / "share"
+
+
+def python_prefix(*, install_root: Path | None = None) -> Path:
+    if install_root is not None:
+        return install_root
+    data = Path(sysconfig.get_path("data"))
+    if data.name == "share":
+        return data.parent
+    return data
+
+
+def completion_targets(*, install_root: Path | None = None) -> list[CompletionTarget]:
+    share = python_share_dir(install_root=install_root)
+    return [
+        CompletionTarget("zsh", share / "zsh" / "site-functions" / _CONFIG.zsh_filename),
+        CompletionTarget(
+            "bash",
+            share / "bash-completion" / "completions" / _CONFIG.bash_filename,
+        ),
+    ]
+
+
+def _script_for_shell(shell: str, cli) -> str:
+    from click.shell_completion import get_completion_class
+
+    shell_class = get_completion_class(shell)
+    if shell_class is None:
+        msg = f"unsupported shell for completion: {shell}"
+        raise ValueError(msg)
+    comp = shell_class(cli, {}, PROG_NAME, CLICK_COMPLETE_VAR)
+    script = comp.source()
+    if not script.endswith("\n"):
+        script += "\n"
+    return script
+
+
+def _record_line(record_path: str, content: bytes) -> str:
+    digest = base64.urlsafe_b64encode(hashlib.sha256(content).digest()).decode().rstrip("=")
+    return f"{record_path},{digest},{len(content)}"
+
+
+def _record_path(install_root: Path, target: Path) -> str:
+    return os.path.relpath(target, install_root).replace(os.sep, "/")
+
+
+def append_record_entries(
+    record_path: Path,
+    installed: list[Path],
+    install_root: Path,
+) -> None:
+    if not installed:
+        return
+    existing = record_path.read_text(encoding="utf-8") if record_path.is_file() else ""
+    lines = [line for line in existing.splitlines() if line.strip()]
+    known = {line.split(",", 1)[0] for line in lines if "," in line}
+    for path in installed:
+        record_key = _record_path(install_root, path)
+        if record_key in known:
+            continue
+        content = path.read_bytes()
+        lines.append(_record_line(record_key, content))
+        known.add(record_key)
+    record_path.write_text("\n".join(lines) + "\n", encoding="utf-8")
+
+
+def write_manifest(dist_info_dir: Path, installed: list[Path]) -> None:
+    manifest = dist_info_dir / MANIFEST_FILENAME
+    manifest.write_text("\n".join(str(path) for path in installed) + "\n", encoding="utf-8")
+
+
+def read_manifest(dist_info_dir: Path | None) -> list[Path]:
+    if dist_info_dir is None:
+        return []
+    manifest = dist_info_dir / MANIFEST_FILENAME
+    if not manifest.is_file():
+        return []
+    return [
+        Path(line.strip())
+        for line in manifest.read_text(encoding="utf-8").splitlines()
+        if line.strip()
+    ]
+
+
+def _site_package_roots() -> list[Path]:
+    roots: list[Path] = []
+    seen: set[Path] = set()
+    for raw in (*site.getsitepackages(), site.getusersitepackages()):
+        if not raw:
+            continue
+        root = Path(raw)
+        if root in seen:
+            continue
+        seen.add(root)
+        roots.append(root)
+    return roots
+
+
+def find_dist_info_dir() -> Path | None:
+    for root in _site_package_roots():
+        if not root.is_dir():
+            continue
+        for pattern in _CONFIG.dist_info_globs:
+            matches = sorted(root.glob(pattern))
+            if matches:
+                return matches[-1]
+    return None
+
+
+def install_root_from_install_lib(install_lib: str | None) -> Path | None:
+    if not install_lib:
+        return None
+    path = Path(install_lib).resolve()
+    if path.name != "site-packages":
+        return None
+    return path.parent.parent.parent
+
+
+def install_completions(
+    cli,
+    *,
+    install_root: Path | None = None,
+    dist_info_dir: Path | None = None,
+) -> list[Path]:
+    root = install_root or python_prefix()
+    scripts = {shell: _script_for_shell(shell, cli) for shell in ("zsh", "bash")}
+    installed: list[Path] = []
+    for target in completion_targets(install_root=root):
+        try:
+            target.path.parent.mkdir(parents=True, exist_ok=True)
+        except OSError:
+            continue
+        if not os.access(target.path.parent, os.W_OK):
+            continue
+        target.path.write_text(scripts[target.shell], encoding="utf-8")
+        installed.append(target.path)
+
+    dist_info = dist_info_dir or find_dist_info_dir()
+    if dist_info is not None:
+        write_manifest(dist_info, installed)
+        record_path = dist_info / "RECORD"
+        if record_path.is_file():
+            append_record_entries(record_path, installed, root)
+    return installed
+
+
+def _completion_script_is_current(path: Path, marker: str) -> bool:
+    if not path.is_file():
+        return False
+    return marker in path.read_text(encoding="utf-8")
+
+
+def completions_installed(*, install_root: Path | None = None) -> bool:
+    for target in completion_targets(install_root=install_root):
+        if target.shell == "zsh" and _completion_script_is_current(
+            target.path,
+            _CONFIG.click_complete_var,
+        ):
+            return True
+    return False
+
+
+def ensure_completions_installed(cli) -> None:
+    if completions_installed():
+        return
+    try:
+        install_completions(cli, dist_info_dir=find_dist_info_dir())
+    except (OSError, ValueError):
+        return
+
+
+def uninstall_completions(*, dist_info_dir: Path | None = None) -> list[Path]:
+    dist_info = dist_info_dir or find_dist_info_dir()
+    removed: list[Path] = []
+    manifest_paths = read_manifest(dist_info)
+    candidates = manifest_paths or [target.path for target in completion_targets()]
+    seen: set[Path] = set()
+    for path in candidates:
+        if path in seen:
+            continue
+        seen.add(path)
+        if path.is_file():
+            path.unlink()
+            removed.append(path)
+
+    if dist_info is not None:
+        record_path = dist_info / "RECORD"
+        if record_path.is_file():
+            root = install_root_from_install_lib(str(dist_info.parent))
+            if root is None:
+                root = dist_info.parent.parent.parent
+            removed_keys = {_record_path(root, path) for path in removed}
+            kept = [
+                line
+                for line in record_path.read_text(encoding="utf-8").splitlines()
+                if line.strip() and line.split(",", 1)[0] not in removed_keys
+            ]
+            record_path.write_text("\n".join(kept) + ("\n" if kept else ""), encoding="utf-8")
+        manifest = dist_info / MANIFEST_FILENAME
+        if manifest.is_file():
+            manifest.unlink()
+    return removed

mytoolkit/commands/self_mgmt.py

@@ -1,6 +1,5 @@
 """Self-management commands for bin."""
 
-import os
 import shutil
 import subprocess
 import sys
@@ -8,14 +7,7 @@ from pathlib import Path
 
 import click
 
-
-# 手动安装的文件清单（pip 管理范围外，uninstall 时需要额外清理）
-_MANUAL_FILES: dict[str, list[Path]] = {
-    "completions": [
-        Path.home() / ".local" / "bin" / "completions" / "_mytoolkit",
-        Path.home() / ".local" / "bin" / "completions" / "mytoolkit.bash",
-    ],
-}
+from mytoolkit.commands.completion_install import uninstall_completions
 
 
 def _get_project_root() -> Path:
@@ -44,59 +36,41 @@ def _install(root: Path) -> None:
 
 
 def _install_completions() -> None:
+    """Install shell completions under the active Python prefix."""
     venv_toolkit = shutil.which("mytoolkit")
     if not venv_toolkit:
-        click.secho("Warning: cannot generate completions (mytoolkit not in PATH)", fg="yellow")
+        click.secho("Warning: cannot install completions (mytoolkit not in PATH)", fg="yellow")
         return
 
-    comp_dir = Path.home() / ".local" / "bin" / "completions"
-    comp_dir.mkdir(parents=True, exist_ok=True)
-    shell = os.environ.get("SHELL", "")
-    if "zsh" in shell:
-        comp_file = comp_dir / "_mytoolkit"
     result = subprocess.run(
-            [venv_toolkit],
-            env={**os.environ, "_MYTOOLKIT_COMPLETE": "zsh_source"},
+        [venv_toolkit, "completion", "install"],
         capture_output=True,
         text=True,
     )
     if result.returncode == 0:
-            comp_file.write_text(result.stdout)
-            click.secho(f"Installed zsh completion: {comp_file}", fg="green")
+        for line in result.stdout.splitlines():
+            click.secho(f"Installed completion: {line}", fg="green")
     else:
-            click.secho("Warning: failed to generate zsh completion", fg="yellow")
-    elif "bash" in shell:
-        comp_file = comp_dir / "mytoolkit.bash"
-        result = subprocess.run(
-            [venv_toolkit],
-            env={**os.environ, "_MYTOOLKIT_COMPLETE": "bash_source"},
-            capture_output=True,
-            text=True,
-        )
-        if result.returncode == 0:
-            comp_file.write_text(result.stdout)
-            click.secho(f"Installed bash completion: {comp_file}", fg="green")
-        else:
-            click.secho("Warning: failed to generate bash completion", fg="yellow")
+        click.secho("Warning: failed to install completions", fg="yellow")
+        if result.stderr:
+            click.secho(result.stderr, fg="yellow")
 
 
 def _uninstall() -> None:
+    # Remove completion scripts first so pip uninstall keeps things clean.
+    try:
+        removed = uninstall_completions()
+        for path in removed:
+            click.secho(f"Removed completion: {path}", fg="green")
+    except (OSError, ValueError) as exc:
+        click.secho(f"Warning: failed to remove completions: {exc}", fg="yellow")
+
     click.secho("Uninstalling mytoolkit package…", fg="cyan")
     subprocess.run(
         [sys.executable, "-m", "pip", "uninstall", "mytoolkit", "-y"],
         check=False,
     )
 
-    removed = 0
-    for paths in _MANUAL_FILES.values():
-        for f in paths:
-            if f.exists() or f.is_symlink():
-                f.unlink()
-                click.secho(f"Removed {f}", fg="green")
-                removed += 1
-    if removed == 0:
-        click.secho("No manual files to clean up.", fg="cyan")
-
 
 @click.command(name="update")
 def update_cmd():

mytoolkit/config.py

@@ -18,10 +18,36 @@ class Config:
         self._data = self._load()
 
     def _migrate_legacy(self) -> None:
-        """One-shot move of legacy bin/config.json into the user config dir."""
-        if _LEGACY_PATH.exists() and not self._config_path.exists():
+        """One-shot move of legacy config files into env.json."""
+        if self._config_path.exists():
+            return
+
+        migrated = False
+
+        # 1) Legacy bundled config.json next to this module.
+        if _LEGACY_PATH.exists():
             self._config_path.parent.mkdir(parents=True, exist_ok=True)
             _LEGACY_PATH.rename(self._config_path)
+            migrated = True
+
+        # 2) Old ~/.mytoolkit/config.json (sectioned layout) -> flat env.json vars.
+        legacy_user = self._config_path.parent / "config.json"
+        if not migrated and legacy_user.exists():
+            try:
+                with open(legacy_user, encoding="utf-8") as f:
+                    data = json.load(f)
+            except (json.JSONDecodeError, OSError):
+                data = {}
+            flat_vars: dict[str, str] = {}
+            for section in ("paths", "keys", "tokens", "other"):
+                section_data = data.get(section)
+                if isinstance(section_data, dict):
+                    flat_vars.update(section_data)
+            if flat_vars:
+                self._data = {"vars": flat_vars}
+                self.save()
+                legacy_user.unlink()
+                migrated = True
 
     def _load(self) -> dict:
         if self._config_path.exists():

mytoolkit/scaffolds/paper/README.md

@@ -11,7 +11,6 @@ fully portable) and compiles with `xelatex` via `latexmk`.
 - `diffpreamble.dtx`: `latexdiff` style preamble
 - `references.bib`: bibliography
 - `figs/`: figures
-- `analysis/`: analysis scripts and data
 - `build/`: build output (auto-generated)
 
 ## Build