/graphify                                             # full pipeline on current directory (HTML viz; add --obsidian for a vault)
/graphify <path>                                      # full pipeline on specific path
/graphify https://github.com/<owner>/<repo>           # clone repo then run full pipeline on it
/graphify https://github.com/<owner>/<repo> --branch <branch>  # clone a specific branch
/graphify <url1> <url2> ...                           # clone multiple repos, build each, merge into one cross-repo graph
/graphify <path> --mode deep                          # thorough extraction, richer INFERRED edges
/graphify <path> --update                             # incremental - re-extract only new/changed files
/graphify <path> --directed                            # build directed graph (preserves edge direction: source→target)
/graphify <path> --whisper-model medium                # use a larger Whisper model for better transcription accuracy
/graphify <path> --cluster-only                       # rerun clustering on existing graph
/graphify <path> --no-viz                             # skip visualization, just report + JSON
/graphify <path> --html                               # (HTML is generated by default - this flag is a no-op)
/graphify <path> --svg                                # also export graph.svg (embeds in Notion, GitHub)
/graphify <path> --graphml                            # export graph.graphml (Gephi, yEd)
/graphify <path> --neo4j                              # generate graphify-out/cypher.txt for Neo4j
/graphify <path> --neo4j-push bolt://localhost:7687   # push directly to Neo4j
/graphify <path> --falkordb                           # generate graphify-out/cypher.txt for FalkorDB
/graphify <path> --falkordb-push falkordb://localhost:6379   # push directly to FalkorDB
/graphify <path> --mcp                                # start MCP stdio server for agent access
/graphify <path> --watch                              # watch folder, auto-rebuild on code changes (no LLM needed)
/graphify <path> --wiki                               # build agent-crawlable wiki (index.md + one article per community)
/graphify <path> --obsidian --obsidian-dir ~/vaults/my-project  # write vault to custom path (e.g. existing vault)
/graphify add <url>                                   # fetch URL, save to ./raw, update graph
/graphify add <url> --author "Name"                   # tag who wrote it
/graphify add <url> --contributor "Name"              # tag who added it to the corpus
/graphify query "<question>"                          # BFS traversal - broad context
/graphify query "<question>" --dfs                    # DFS - trace a specific path
/graphify query "<question>" --budget 1500            # cap answer at N tokens
/graphify path "AuthModule" "Database"                # shortest path between two concepts
/graphify explain "SwinTransformer"                   # plain-language explanation of a node

# Detect the correct Python interpreter (handles uv tool, pipx, venv, system installs)
PYTHON=""
GRAPHIFY_BIN=$(which graphify 2>/dev/null)
# 1. uv tool installs — most reliable on modern Mac/Linux
if [ -z "$PYTHON" ] && command -v uv >/dev/null 2>&1; then
    _UV_PY=$(uv tool run --from graphifyy python -c "import sys; print(sys.executable)" 2>/dev/null)
    if [ -n "$_UV_PY" ]; then PYTHON="$_UV_PY"; fi
fi
# 2. Read shebang from graphify binary (pipx and direct pip installs)
if [ -z "$PYTHON" ] && [ -n "$GRAPHIFY_BIN" ]; then
    _SHEBANG=$(head -1 "$GRAPHIFY_BIN" | tr -d '#!')
    case "$_SHEBANG" in
        *[!a-zA-Z0-9/_.@-]*) ;;
        *) "$_SHEBANG" -c "import graphify" 2>/dev/null && PYTHON="$_SHEBANG" ;;
    esac
fi
# 3. Fall back to python3
if [ -z "$PYTHON" ]; then PYTHON="python3"; fi
if ! "$PYTHON" -c "import graphify" 2>/dev/null; then
    if command -v uv >/dev/null 2>&1; then
        uv tool install --upgrade graphifyy -q 2>&1 | tail -3
        _UV_PY=$(uv tool run --from graphifyy python -c "import sys; print(sys.executable)" 2>/dev/null)
        if [ -n "$_UV_PY" ]; then PYTHON="$_UV_PY"; fi
    else
        "$PYTHON" -m pip install graphifyy -q 2>/dev/null \
          || "$PYTHON" -m pip install graphifyy -q --break-system-packages 2>&1 | tail -3
    fi
fi
# Write interpreter path for all subsequent steps (persists across invocations)
mkdir -p graphify-out
"$PYTHON" -c "import sys; open('graphify-out/.graphify_python', 'w', encoding='utf-8').write(sys.executable)"
# Save scan root so `graphify update` (no args) knows where to look next time.
# The scan path is passed through a quoted heredoc, never substituted into the
# command line itself: a bare `cd <path>` (or an unquoted heredoc, which
# still expands $()/backticks in its body) would let a malicious path execute
# as shell code the moment this line runs.
"$PYTHON" -c "import os, sys; out_path = os.path.abspath('graphify-out/.graphify_root'); os.chdir(sys.stdin.readline().rstrip('\n')); open(out_path, 'w', encoding='utf-8').write(os.getcwd())" <<'GRAPHIFY_ROOT_EOF'
INPUT_PATH
GRAPHIFY_ROOT_EOF

$(cat graphify-out/.graphify_python) -c "
import json
from graphify.detect import detect
from pathlib import Path
result = detect(Path('INPUT_PATH'))
# Write the sidecar from Python, not a shell redirect, so the same block renders
# on PowerShell hosts without console-encoding drift (#2528).
Path('graphify-out/.graphify_detect.json').write_text(json.dumps(result, ensure_ascii=False), encoding=\"utf-8\")
print(f'Detected {result[\"total_files\"]} files')
"

Corpus: X files · ~Y words
  code:     N files (.py .ts .go ...)
  docs:     N files (.md .txt ...)
  papers:   N files (.pdf ...)
  images:   N files
  video:    N files (.mp4 .mp3 ...)

$(cat graphify-out/.graphify_python) -c "
import sys, json
from graphify.extract import collect_files, extract
from pathlib import Path
import json

code_files = []
detect = json.loads(Path('graphify-out/.graphify_detect.json').read_text(encoding=\"utf-8\"))
for f in detect.get('files', {}).get('code', []):
    code_files.extend(collect_files(Path(f)) if Path(f).is_dir() else [Path(f)])

if code_files:
    result = extract(code_files, cache_root=Path('INPUT_PATH'))
    Path('graphify-out/.graphify_ast.json').write_text(json.dumps(result, indent=2, ensure_ascii=False), encoding=\"utf-8\")
    print(f'AST: {len(result[\"nodes\"])} nodes, {len(result[\"edges\"])} edges')
else:
    Path('graphify-out/.graphify_ast.json').write_text(json.dumps({'nodes':[],'edges':[],'input_tokens':0,'output_tokens':0}, ensure_ascii=False), encoding=\"utf-8\")
    print('No code files - skipping AST extraction')
"

$(cat graphify-out/.graphify_python) -c "
import json
from pathlib import Path
Path('graphify-out/.graphify_semantic.json').write_text(json.dumps({'nodes':[],'edges':[],'hyperedges':[],'input_tokens':0,'output_tokens':0}), encoding='utf-8')
"

$(cat graphify-out/.graphify_python) -c "
import json
from graphify.cache import check_semantic_cache
from pathlib import Path

detect = json.loads(Path('graphify-out/.graphify_detect.json').read_text(encoding=\"utf-8\"))
# Only content files go to semantic extraction. Code is already covered structurally
# by the AST pass (Part A); flattening every category here makes subagents re-read
# every source file (#1392). Video is transcribed to a document in Step 2.5 first.
all_files = [f for cat in ('document', 'paper', 'image') for f in detect['files'].get(cat, [])]

cached_nodes, cached_edges, cached_hyperedges, uncached = check_semantic_cache(all_files, root='INPUT_PATH', prompt_file='SPEC_PATH')

# Always (re)write the cache file: write hits, else DELETE any leftover from a prior
# run so Part C never merges a stale .graphify_cached.json (#1392).
if cached_nodes or cached_edges or cached_hyperedges:
    Path('graphify-out/.graphify_cached.json').write_text(json.dumps({'nodes': cached_nodes, 'edges': cached_edges, 'hyperedges': cached_hyperedges}, ensure_ascii=False), encoding=\"utf-8\")
else:
    Path('graphify-out/.graphify_cached.json').unlink(missing_ok=True)
Path('graphify-out/.graphify_uncached.txt').write_text('\n'.join(uncached), encoding=\"utf-8\")
print(f'Cache: {len(all_files)-len(uncached)} files hit, {len(uncached)} files need extraction')
"

[Agent tool call 1: files 1-15, subagent_type="general-purpose"]
[Agent tool call 2: files 16-30, subagent_type="general-purpose"]
[Agent tool call 3: files 31-45, subagent_type="general-purpose"]

PROJECT_ROOT=$(pwd)  # cwd — where Part C globs graphify-out/ (NOT .graphify_root/scan dir, #1392)
# Then for chunk N: CHUNK_PATH="${PROJECT_ROOT}/graphify-out/.graphify_chunk_0N.json"

$(cat graphify-out/.graphify_python) -c "
import json, glob
from pathlib import Path

chunks = sorted(glob.glob('graphify-out/.graphify_chunk_*.json'))
all_nodes, all_edges, all_hyperedges = [], [], []
total_in, total_out = 0, 0
for c in chunks:
    d = json.loads(Path(c).read_text(encoding=\"utf-8\"))
    all_nodes += d.get('nodes', [])
    all_edges += d.get('edges', [])
    all_hyperedges += d.get('hyperedges', [])
    total_in += d.get('input_tokens', 0)
    total_out += d.get('output_tokens', 0)
Path('graphify-out/.graphify_semantic_new.json').write_text(json.dumps({
    'nodes': all_nodes, 'edges': all_edges, 'hyperedges': all_hyperedges,
    'input_tokens': total_in, 'output_tokens': total_out,
}, indent=2, ensure_ascii=False), encoding=\"utf-8\")
print(f'Merged {len(chunks)} chunks: {total_in:,} in / {total_out:,} out tokens')
"

$(cat graphify-out/.graphify_python) -c "
import json
from graphify.cache import save_semantic_cache
from pathlib import Path

new = json.loads(Path('graphify-out/.graphify_semantic_new.json').read_text(encoding=\"utf-8\")) if Path('graphify-out/.graphify_semantic_new.json').exists() else {'nodes':[],'edges':[],'hyperedges':[]}
uncached = [line for line in Path('graphify-out/.graphify_uncached.txt').read_text(encoding=\"utf-8\").splitlines() if line]
saved = save_semantic_cache(new.get('nodes', []), new.get('edges', []), new.get('hyperedges', []), root='INPUT_PATH', allowed_source_files=uncached, prompt_file='SPEC_PATH')
print(f'Cached {saved} files')
"

$(cat graphify-out/.graphify_python) -c "
import json
from pathlib import Path

cached = json.loads(Path('graphify-out/.graphify_cached.json').read_text(encoding=\"utf-8\")) if Path('graphify-out/.graphify_cached.json').exists() else {'nodes':[],'edges':[],'hyperedges':[]}
new = json.loads(Path('graphify-out/.graphify_semantic_new.json').read_text(encoding=\"utf-8\")) if Path('graphify-out/.graphify_semantic_new.json').exists() else {'nodes':[],'edges':[],'hyperedges':[]}

all_nodes = cached['nodes'] + new.get('nodes', [])
all_edges = cached['edges'] + new.get('edges', [])
all_hyperedges = cached.get('hyperedges', []) + new.get('hyperedges', [])
seen = set()
deduped = []
for n in all_nodes:
    if n['id'] not in seen:
        seen.add(n['id'])
        deduped.append(n)

merged = {
    'nodes': deduped,
    'edges': all_edges,
    'hyperedges': all_hyperedges,
    'input_tokens': new.get('input_tokens', 0),
    'output_tokens': new.get('output_tokens', 0),
}
Path('graphify-out/.graphify_semantic.json').write_text(json.dumps(merged, indent=2, ensure_ascii=False), encoding=\"utf-8\")
print(f'Extraction complete - {len(deduped)} nodes, {len(all_edges)} edges ({len(cached[\"nodes\"])} from cache, {len(new.get(\"nodes\",[]))} new)')
"

$(cat graphify-out/.graphify_python) -c "
import sys, json
from pathlib import Path

ast = json.loads(Path('graphify-out/.graphify_ast.json').read_text(encoding=\"utf-8\"))
sem = json.loads(Path('graphify-out/.graphify_semantic.json').read_text(encoding=\"utf-8\"))

# Merge: AST nodes first, semantic nodes deduplicated by id
seen = {n['id'] for n in ast['nodes']}
merged_nodes = list(ast['nodes'])
for n in sem['nodes']:
    if n['id'] not in seen:
        merged_nodes.append(n)
        seen.add(n['id'])

merged_edges = ast['edges'] + sem['edges']
merged_hyperedges = sem.get('hyperedges', [])
merged = {
    'nodes': merged_nodes,
    'edges': merged_edges,
    'hyperedges': merged_hyperedges,
    'input_tokens': sem.get('input_tokens', 0),
    'output_tokens': sem.get('output_tokens', 0),
}
Path('graphify-out/.graphify_extract.json').write_text(json.dumps(merged, indent=2, ensure_ascii=False), encoding=\"utf-8\")
total = len(merged_nodes)
edges = len(merged_edges)
print(f'Merged: {total} nodes, {edges} edges ({len(ast[\"nodes\"])} AST + {len(sem[\"nodes\"])} semantic)')
"

mkdir -p graphify-out
$(cat graphify-out/.graphify_python) -c "
import sys, json
from graphify.build import build_from_json
from graphify.cluster import cluster, score_all
from graphify.analyze import god_nodes, surprising_connections, suggest_questions
from graphify.report import generate
from graphify.export import to_json
from pathlib import Path

extraction = json.loads(Path('graphify-out/.graphify_extract.json').read_text(encoding=\"utf-8\"))
detection  = json.loads(Path('graphify-out/.graphify_detect.json').read_text(encoding=\"utf-8\"))

# root= mirrors the --update runbook (#1361): relativize source_file to the same
# base so the full build and incremental --update never drift apart on re-extract.
G = build_from_json(extraction, root='INPUT_PATH', directed=IS_DIRECTED)
# Guard BEFORE any write: an empty extraction must not clobber a good graph.json /
# GRAPH_REPORT.md / analysis sidecar. Check immediately after build (#1392).
if G.number_of_nodes() == 0:
    print('ERROR: Graph is empty - extraction produced no nodes.')
    print('Possible causes: all files were skipped, binary-only corpus, or extraction failed.')
    raise SystemExit(1)
communities = cluster(G)
cohesion = score_all(G, communities)
tokens = {'input': extraction.get('input_tokens', 0), 'output': extraction.get('output_tokens', 0)}
gods = god_nodes(G)
surprises = surprising_connections(G, communities)
labels = {cid: 'Community ' + str(cid) for cid in communities}
# Placeholder questions - regenerated with real labels in Step 5
questions = suggest_questions(G, communities, labels)

# Export FIRST and honor the #479 shrink-guard: to_json returns False (writing
# nothing) when the new graph is smaller than the existing graph.json. Only write
# GRAPH_REPORT.md + the analysis sidecar when the graph was actually written, so
# they never describe a graph that graph.json doesn't contain (#1392).
wrote = to_json(G, communities, 'graphify-out/graph.json')
if not wrote:
    print('ERROR: refused to shrink graphify-out/graph.json (existing graph has more nodes; #479).')
    print('If this shrink is intentional (you deleted files), re-run a full build with --force.')
    raise SystemExit(1)
report = generate(G, communities, cohesion, labels, gods, surprises, detection, tokens, 'INPUT_PATH', suggested_questions=questions)
Path('graphify-out/GRAPH_REPORT.md').write_text(report, encoding=\"utf-8\")
analysis = {
    'communities': {str(k): v for k, v in communities.items()},
    'cohesion': {str(k): v for k, v in cohesion.items()},
    'gods': gods,
    'surprises': surprises,
    'questions': questions,
}
Path('graphify-out/.graphify_analysis.json').write_text(json.dumps(analysis, indent=2, ensure_ascii=False), encoding=\"utf-8\")
print(f'Graph: {G.number_of_nodes()} nodes, {G.number_of_edges()} edges, {len(communities)} communities')
"

$(cat graphify-out/.graphify_python) -c "
import json
from pathlib import Path
from graphify.diagnostics import diagnose_extraction, format_diagnostic_report

extraction = json.loads(Path('graphify-out/.graphify_extract.json').read_text(encoding=\"utf-8\"))
summary = diagnose_extraction(extraction, directed=IS_DIRECTED, root='INPUT_PATH')
print(format_diagnostic_report(summary))
flags = [f'{summary[k]} {label}' for k, label in (
    ('dangling_endpoint_edges', 'dangling-endpoint edges'),
    ('missing_endpoint_edges', 'missing-endpoint edges'),
    ('self_loop_edges', 'self-loop edges'),
    ('directed_same_endpoint_collapsed_edges', 'collapsed (directed) edges'),
    ('undirected_same_endpoint_collapsed_edges', 'collapsed (undirected) edges'),
) if summary.get(k, 0)]
print('GRAPH HEALTH WARNING: ' + '; '.join(flags) + ' - graph may be incomplete/corrupt.' if flags else 'Graph health: OK (no dangling/missing/collapsed edges).')
"

$(cat graphify-out/.graphify_python) -c "
import sys, json
from graphify.build import build_from_json
from graphify.cluster import score_all
from graphify.analyze import god_nodes, surprising_connections, suggest_questions
from graphify.report import generate
from graphify.export import to_json
from pathlib import Path

extraction = json.loads(Path('graphify-out/.graphify_extract.json').read_text(encoding=\"utf-8\"))
detection  = json.loads(Path('graphify-out/.graphify_detect.json').read_text(encoding=\"utf-8\"))
analysis   = json.loads(Path('graphify-out/.graphify_analysis.json').read_text(encoding=\"utf-8\"))

# root= as in Step 4 / the --update runbook (#1361) — same base for node-key parity.
G = build_from_json(extraction, root='INPUT_PATH', directed=IS_DIRECTED)
communities = {int(k): v for k, v in analysis['communities'].items()}
cohesion = {int(k): v for k, v in analysis['cohesion'].items()}
tokens = {'input': extraction.get('input_tokens', 0), 'output': extraction.get('output_tokens', 0)}

# LABELS - replace these with the names you chose above
labels = LABELS_DICT

# Regenerate questions with real community labels (labels affect question phrasing)
questions = suggest_questions(G, communities, labels)

report = generate(G, communities, cohesion, labels, analysis['gods'], analysis['surprises'], detection, tokens, 'INPUT_PATH', suggested_questions=questions)
Path('graphify-out/GRAPH_REPORT.md').write_text(report, encoding=\"utf-8\")
Path('graphify-out/.graphify_labels.json').write_text(json.dumps({str(k): v for k, v in labels.items()}, ensure_ascii=False), encoding=\"utf-8\")
# Re-export so graph.json nodes carry the curated community_name (#2490).
# Same extraction as Step 4, so the #479 shrink-guard passes on node count;
# if it still refuses, surface the guard message - do not force past it.
wrote = to_json(G, communities, 'graphify-out/graph.json', community_labels=labels)
if not wrote:
    print('ERROR: refused to shrink graphify-out/graph.json (existing graph has more nodes; #479).')
    print('If this shrink is intentional (you deleted files), re-run a full build with --force.')
print('Report updated with community labels')
"

graphify export obsidian
# or with custom dir: graphify export obsidian --dir ~/vaults/my-project

graphify export html  # auto-aggregates to community view if graph > 5000 nodes
# or: graphify export html --no-viz

$(cat graphify-out/.graphify_python) -c "
import json
from pathlib import Path
from datetime import datetime, timezone
from graphify.detect import save_manifest

# Save manifest for --update
detect = json.loads(Path('graphify-out/.graphify_detect.json').read_text(encoding=\"utf-8\"))
extract = json.loads(Path('graphify-out/.graphify_extract.json').read_text(encoding=\"utf-8\"))
# In --update mode, 'all_files' carries the full corpus; 'files' is the changed
# subset. Full-rebuild mode populates only 'files', so the fallback handles that.
# root= relativizes the manifest keys to the scan root (same base as the build),
# so the on-disk manifest is portable across clones/machines and a later --update
# matches cached files instead of missing every one (#1417).
#
# Only stamp semantic files (docs/papers/images) that ACTUALLY produced output:
# a detected file whose chunk failed or was omitted must stay unstamped so the
# next --update re-queues it, otherwise it is marked done and its content is lost
# forever (#2015). This mirrors the library extract path exactly
# (cli._stamped_manifest_files + clear_semantic + scan_corpus); do not stamp the
# raw corpus. Code files are always stamped (AST is deterministic); only semantic
# types are gated on output.
from graphify.cli import _stamped_manifest_files
_corpus = detect.get('all_files') or detect['files']
_manifest_files = _stamped_manifest_files(_corpus, extract, Path('INPUT_PATH'))
# Files dispatched this run (the changed subset) but NOT stamped above still carry
# a stale semantic_hash from a prior run; clear it so detect_incremental re-queues
# them instead of reading them as unchanged (#1948).
_sem_types = ('document', 'paper', 'image')
_dispatched = {f for t, fl in detect['files'].items() if t in _sem_types for f in fl}
_stamped = {f for fl in _manifest_files.values() for f in fl}
_cleared = _dispatched - _stamped
# scan_corpus = the RAW full corpus (not the stamp-filtered subset) so in-root
# files newly excluded since last run are dropped rather than masquerading as
# deletions; untouched files' prior rows are still preserved (#1908).
_scan = {f for fl in _corpus.values() for f in fl}
save_manifest(_manifest_files, root='INPUT_PATH', scan_corpus=_scan, clear_semantic=_cleared or None)

# Update cumulative cost tracker
input_tok = extract.get('input_tokens', 0)
output_tok = extract.get('output_tokens', 0)

cost_path = Path('graphify-out/cost.json')
if cost_path.exists():
    cost = json.loads(cost_path.read_text(encoding=\"utf-8\"))
else:
    cost = {'runs': [], 'total_input_tokens': 0, 'total_output_tokens': 0}

cost['runs'].append({
    'date': datetime.now(timezone.utc).isoformat(),
    'input_tokens': input_tok,
    'output_tokens': output_tok,
    'files': detect.get('total_files', 0),
})
cost['total_input_tokens'] += input_tok
cost['total_output_tokens'] += output_tok
cost_path.write_text(json.dumps(cost, indent=2, ensure_ascii=False), encoding=\"utf-8\")

print(f'This run: {input_tok:,} input tokens, {output_tok:,} output tokens')
print(f'All time: {cost[\"total_input_tokens\"]:,} input, {cost[\"total_output_tokens\"]:,} output ({len(cost[\"runs\"])} runs)')
"
rm -f graphify-out/.graphify_detect.json graphify-out/.graphify_extract.json graphify-out/.graphify_ast.json graphify-out/.graphify_semantic.json graphify-out/.graphify_analysis.json
find graphify-out -maxdepth 1 -name '.graphify_chunk_*.json' -delete 2>/dev/null
rm -f graphify-out/.needs_update 2>/dev/null || true

Graph complete. Outputs in PATH_TO_DIR/graphify-out/

  graph.html            - interactive graph, open in browser
  GRAPH_REPORT.md       - audit report
  graph.json            - raw graph data
  obsidian/             - Obsidian vault (only if --obsidian was given)

if [ ! -f graphify-out/.graphify_python ]; then
    GRAPHIFY_BIN=$(which graphify 2>/dev/null)
    if [ -n "$GRAPHIFY_BIN" ]; then
        PYTHON=$(head -1 "$GRAPHIFY_BIN" | tr -d '#!')
        case "$PYTHON" in *[!a-zA-Z0-9/_.@-]*) PYTHON="python3" ;; esac
    else
        PYTHON="python3"
    fi
    mkdir -p graphify-out
    "$PYTHON" -c "import sys; open('graphify-out/.graphify_python', 'w', encoding='utf-8').write(sys.executable)"
fi

graphify query "<question>"