move CLI command files into cli/commands/ subdirectory

[noanflaherty]

Summary

• Moved 26 CLI command registration files from assistant/src/cli/ into assistant/src/cli/commands/ to separate command definitions from shared utilities and infrastructure
• Updated all relative imports in moved files, program.ts, and 6 test files
• No functional changes — pure file reorganization with import path updates

Original prompt

Help me move all of these files into assistant/src/cli/commands so that all remaining files in assistant/src/cli are more like utility functions, and other things, not commands that need registering.

Generated with Claude Code

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[devin-ai-integration]

Devin Review found 4 potential issues.

View 3 additional findings in Devin Review.

[chatgpt-codex-connector]

💡 Codex Review

vellum-assistant/assistant/src/cli/commands/dev.ts

Line 100 in 5726d7e

const mainPath = `${import.meta.dirname}/../daemon/main.ts`;

Point dev launcher to daemon main entry

After moving this file into cli/commands, import.meta.dirname is one directory deeper, so ../daemon/main.ts now resolves to assistant/src/cli/daemon/main.ts (which does not exist). That makes assistant dev (with or without --watch) fail when it tries to spawn bun run against the wrong script path, so the dev command no longer starts the assistant.

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vellum-assistant/assistant/src/cli/commands/doctor.ts

Line 330 in 5726d7e

let fullPath = `${dir}/../../node_modules/${wasm.pkg}/${wasm.file}`;

Resolve doctor WASM path from commands directory

This relative path was correct before the move, but from assistant/src/cli/commands/doctor.ts the expression ../../node_modules/... points to assistant/src/node_modules instead of assistant/node_modules. In source runs, assistant doctor will now falsely report missing Tree-sitter WASM files even when dependencies are installed, which degrades diagnostics reliability.

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vellum-assistant/assistant/src/cli/commands/skills.ts

Line 43 in 5726d7e

const candidate = join(import.meta.dir, "..", "..", "..", "skills");

Update dev skills catalog lookup to new file depth

With the command file moved under cli/commands, this ../../../skills lookup now resolves to assistant/skills instead of the repo-level skills/ directory. When VELLUM_DEV is enabled, getRepoSkillsDir() will miss the local catalog and disable repo-local skill discovery, which breaks local development/offline workflows for assistant skills.

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[noanflaherty]

Addressed in #14257