update-tools

Academic Writer — Update Tools

Modify which integrations are enabled without re-running the full initialization.

Load Current Profile

if [ -f .academic-helper/profile.md ]; then
  cat .academic-helper/profile.md
else
  echo "No profile found. Run /academic-writer:init first."
  exit 1
fi

Parse the current tools object from the profile. If the profile has no tools key (legacy profile), treat all tools as not configured.

Tool Registry

Run detection for every tool in the registry, regardless of current status:

1. Candlekeep (candlekeep)

command -v ck >/dev/null 2>&1 && echo "DETECTED" || echo "NOT_DETECTED"

2. Agentic-Search-Vectorless (agentic-search-vectorless)

curl -s --max-time 3 http://localhost:8000/health 2>/dev/null && echo "DETECTED" || echo "NOT_DETECTED"

3. Cognetivy (cognetivy)

command -v cognetivy >/dev/null 2>&1 && echo "DETECTED" || echo "NOT_DETECTED"

4. NotebookLM (notebooklm)

command -v nlm >/dev/null 2>&1 && nlm login --check 2>/dev/null && echo "DETECTED" || echo "NOT_DETECTED"

Present Current State

Show a table with current status and detection:

"Here are your current tool integrations:

#	Tool	Currently	Detected	Setup
1	Candlekeep	✓ Enabled / ✗ Disabled	✓ / ✗	https://github.com/romiluz13/candlekeep
2	Agentic-Search-Vectorless	✓ Running / ✗ Not running	✓ / ✗	localhost:8000
3	Cognetivy	✓ Enabled / ✗ Disabled	✓ / ✗	Built-in (.cognetivy/)
4	NotebookLM	✓ Enabled / ✗ Disabled	✓ / ✗	https://github.com/jacob-bd/notebooklm-mcp-cli

What would you like to change? You can:

• Enable a tool by number or name (I'll help install if not detected)
• Disable a tool by number or name
• Say 'done' when finished"

Process Changes

For each tool the user wants to enable:

1. If not detected, show the setup URL and walk them through installation
2. Re-run the detection command to confirm
3. Only mark as enabled once detected

For each tool the user wants to disable:

1. Mark it as disabled immediately
2. Warn if it affects existing sources: "Note: disabling Candlekeep won't delete your indexed sources, but new source management will need to be done manually."

Save Updated Profile

Update ONLY the tools key and updatedAt in the profile. Preserve all other fields:

python3 << 'PYTHON'
import re, json
from datetime import datetime

PROFILE_PATH = '.academic-helper/profile.md'

with open(PROFILE_PATH) as f:
    content = f.read()

# Parse frontmatter scalars and lists
profile = {}
fm_match = re.match(r'^---\n(.*?)\n---', content, re.DOTALL)
if fm_match:
    fm_text = fm_match.group(1)
    i, fm_lines = 0, fm_text.split('\n')
    while i < len(fm_lines):
        line = fm_lines[i]
        kv = re.match(r'^([\w-]+): (.+)$', line)
        ko = re.match(r'^([\w-]+):\s*$', line)
        if kv:
            k, v = kv.group(1), kv.group(2).strip()
            profile[k] = None if v == 'null' else ([] if v == '[]' else v)
            i += 1
        elif ko and i + 1 < len(fm_lines) and fm_lines[i + 1].startswith('  - '):
            k = ko.group(1)
            items = []
            i += 1
            while i < len(fm_lines) and fm_lines[i].startswith('  - '):
                items.append(fm_lines[i][4:])
                i += 1
            profile[k] = items
        else:
            i += 1

# Parse JSON sections
for m in re.finditer(r'^## (.+?)\n+```json\n(.*?)\n```', content, re.MULTILINE | re.DOTALL):
    heading = m.group(1).strip().lower().replace(' ', '')
    try:
        parsed = json.loads(m.group(2))
        mapping = {'tools': 'tools', 'stylefingerprint': 'styleFingerprint',
                   'sources': 'sources', 'articlestructure': 'articleStructure',
                   'outputformatpreferences': 'outputFormatPreferences'}
        if heading in mapping:
            profile[mapping[heading]] = parsed
    except Exception:
        pass

# Update tools — replace TOOL_CONFIG with actual selections
profile['tools'] = TOOL_CONFIG
profile['updatedAt'] = datetime.now().isoformat()

# Write profile.md
scalar_keys = ['fieldOfStudy', 'citationStyle', 'targetLanguage', 'updatedAt', 'createdAt']
list_keys = ['abstractLanguages', 'analyzedArticles']
json_sections = [
    ('tools', 'Tools'), ('outputFormatPreferences', 'Output Format Preferences'),
    ('styleFingerprint', 'Style Fingerprint'), ('articleStructure', 'Article Structure'),
    ('sources', 'Sources'),
]
lines = ['# Academic Writer Profile', '', '---']
for k in scalar_keys:
    if k in profile and profile[k] is not None:
        lines.append(f'{k}: {profile[k]}')
for k in list_keys:
    v = profile.get(k) or []
    if not v:
        lines.append(f'{k}: []')
    else:
        lines.append(f'{k}:')
        for item in v:
            lines.append(f'  - {item}')
lines.extend(['---', ''])
for k, heading in json_sections:
    if k in profile and profile[k] is not None:
        lines.extend([f'## {heading}', '', '```json',
                      json.dumps(profile[k], indent=2, ensure_ascii=False), '```', ''])

with open(PROFILE_PATH, 'w') as f:
    f.write('\n'.join(lines))

print("Tools updated successfully.")
PYTHON

Replace TOOL_CONFIG with the actual tools dict, e.g.:

{
  "candlekeep": { "enabled": true, "version": "detected" },
  "agentic-search-vectorless": { "enabled": true, "port": 8000 },
  "cognetivy": { "enabled": true, "version": "detected" },
  "notebooklm": { "enabled": true, "version": "detected" }
}

Confirm

"Done! Your tools are now:

[list each tool with ✓/✗ status]

These changes take effect immediately for /academic-writer:write. If you enabled Candlekeep and haven't indexed sources yet, run /academic-writer:init to add them."