Workflow

📊 Visual Overview

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🗺️ Overview

⚠️

Enforced by hooks Native tools (Read, Grep, Glob, Edit, Write) are blocked by PreToolUse hooks unless a c3_* tool was called first. Violating the workflow order causes immediate tool denials — not warnings.

#	Step	Tool	When
1	Recall	`c3_memory(action='recall')`	Before any multi-step or context-dependent task
2	Search	`c3_search(action='code\|files\|semantic')`	Before ANY file discovery or content search
3	Map + Read	`c3_compress(mode='map')` → `c3_read(symbols=…)`	Before reading any file content
4	Impact	`c3_impact(target='symbol')`	Before editing shared symbols — check blast radius
5	Edit	`c3_edit(file, old, new, summary)`	All file modifications
6	Filter	`c3_filter(text=…)`	Terminal output >10 lines or log files
7	Validate	`c3_validate(file_path)`	After every edit; type check auto-runs if pyright/tsc installed
8	Log	`c3_session(action='log')`	After decisions; snapshot before /clear
+	Bitbucket	`c3_bitbucket(action='list_prs')`	v2.30.0 — see/act on PRs, branches, builds, repo admin on enterprise Bitbucket Data Center. Full guide →
+	Cross-project	`c3_project(action='list')`	v2.31.0 — discover and operate on OTHER c3-installed projects; reads run free, writes need `allow_write=true`. Tool card →
+	Sub-projects	`c3 sub add <folder>`	v2.44.0 — link child projects living inside a parent; federated search/memory + Hub management. Section →

1

Recall Memory

Recover context from previous sessions before doing anything

c3_memory

The first thing Claude should do at the start of any non-trivial task. This loads relevant facts from the persistent memory store — architecture decisions, conventions, ongoing work, gotchas discovered in prior sessions.

c3_memory(action='recall', query='authentication system refactor')

When to recall

Start of any multi-step task
When the task touches a system you've worked on before
When you suspect there are architecture decisions or gotchas to be aware of

When you can skip

Trivial one-off tasks (rename a variable, fix a typo)
Brand new projects with no prior sessions

💡

Use a specific query matching your task — "recall" pulls the top-k most relevant facts by semantic similarity. A vague query returns less useful results.

2

Search First

Always discover files and code via c3_search — never Grep/Glob directly

c3_search

Action	Use case
code	TF-IDF code search — find functions, classes, patterns by content
files	File discovery — find files by name, extension, path pattern
semantic	Embedding-based similarity search — find conceptually related code
exact	Regex-based exact search — when you know the literal string

❌ Wrong

# Never start with native tools
Grep(pattern='AuthMiddleware')
Glob(pattern='**/*.py')

✅ Correct

c3_search(query='AuthMiddleware', action='code')
c3_search(query='*.py auth', action='files')

prefetch=True

Pass prefetch=True to auto-compress the top result files in parallel, saving a round-trip:

c3_search(query='session manager', action='code', prefetch=True)

3

Map then Read

Get a structural overview first, then read only what you need

c3_compress + c3_read

Reading a whole file wastes tokens. The correct pattern is: compress to get the map, then read only the specific symbols or lines you need.

❌ Wrong

# Reading entire files
Read(file_path='services/session_manager.py')

✅ Correct

# Map → targeted read
c3_compress(file_path='services/session_manager.py', mode='map')
c3_read(file_path='services/session_manager.py', symbols=['SessionManager.save'])

Compress modes

Mode	Output	Best for
map	Line-range map of all symbols (functions, classes, constants)	Understanding file structure before reading
dense_map	Same as map but with docstrings included	When you need a bit more context per symbol
smart	Adaptive compression — keeps important sections	General-purpose read when map is insufficient
diff	Show what changed recently (git diff aware)	Reviewing recent changes
bug_scan	Highlight suspicious patterns	Quick bug-hunting pass

Batch compress

# Compress multiple files in one call
c3_compress(file_path='services/memory.py,services/agents.py', mode='map')

4

Impact Check

Know the blast radius before editing shared symbols

c3_impact

Before renaming, removing, or changing the signature of any function or class used across files, run c3_impact to find every call site. A HIGH risk result means all those files need updating in the same edit pass — skipping this step is how silent breakages happen.

# Check blast radius before renaming a shared function
c3_impact(target='handle_memory', file_path='cli/tools/memory.py')

# Check what's affected AND has uncommitted changes
c3_impact(target='MemoryStore', mode='unstaged')

When to skip

Skip c3_impact when editing purely local symbols (private helpers, inner functions, one-off scripts). Use it for anything in a shared service, public API, or imported across files.

⚠️

A HIGH risk result (7+ files) means the edit isn't isolated — plan to update all call sites in the same session before reporting done.

5

Edit via C3

Atomic read-patch-write-log — always c3_edit, never native Edit

c3_edit

c3_edit does read + patch + write + edit ledger log in one step. It also validates the old_string match before writing. If the literal match fails but the strings differ only by unicode lookalikes (curly quotes, em/en-dashes, NBSP), c3_edit retries with a 1:1 normalized match and tags the response [unicode-normalized].

c3_edit(
  file_path='services/auth.py',
  old_string='return token.expiry > now',
  new_string='return token.expiry > now + timedelta(seconds=CLOCK_SKEW)',
  summary='Add clock skew buffer to token expiry check'
)

Batching edits to the same file

Use the edits=[] parameter to apply multiple patches to one file in one call:

c3_edit(
  file_path='src/config.py',
  edits=[
    {"old_string": "DEBUG = True",  "new_string": "DEBUG = False"},
    {"old_string": "HOST = 'localhost'", "new_string": "HOST = '0.0.0.0'"}
  ],
  summary='Production config hardening'
)

Parallel edits across files

# Call c3_edit for multiple files in parallel (same message, different files)
c3_edit(file_path='src/a.py', old_string='...', new_string='...', summary='...')
c3_edit(file_path='src/b.py', old_string='...', new_string='...', summary='...')

6

Filter Output

Extract signal from noisy terminal output and log files

c3_filter

Any terminal output longer than ~10 lines should be passed through c3_filter to extract only the relevant signal before including it in context.

# Filter raw terminal output
c3_filter(text="<long test output here>")

# Filter a log file
c3_filter(file_path=".c3/sessions/session_001.json", pattern="error|warning")

💡

c3_filter is especially useful after running tests, build commands, or any operation that produces verbose output. It strips noise and returns structured signal.

7

Validate

Syntax + type check every edited file before reporting done

c3_validate

Always call c3_validate after edits. Never report "done" without validation. A syntax error introduced silently is worse than no change at all. If pyright (Python) or tsc (TypeScript) is on your PATH, C3 also runs a deep type check automatically and surfaces type errors as advisory warnings alongside the PASS result.

# Single file
c3_validate(file_path='services/auth.py')

# Batch — comma-separated (runs in parallel internally)
c3_validate(file_path='services/auth.py,services/session.py,cli/c3.py')

Supported languages

Python (.py) JavaScript (.js .mjs) TypeScript (.ts .tsx) HTML (.html) CSS (.css) JSON (.json) TOML (.toml) YAML (.yml .yaml) Bash (.sh)

8

Log & Snapshot

Persist decisions and context so the next session starts informed

c3_session

Log a decision

c3_session(action='log', data='Chose JWT over session cookies — easier horizontal scaling')

Snapshot before /clear

Always snapshot before running /clear. This saves the full session state so the next session can restore it.

c3_session(action='snapshot')
# Then in Claude Code: /clear

Auto-snapshot on session end

C3 automatically captures a snapshot when a session ends — including Ctrl+C, natural stop, and max-turn exits. This is handled by a Stop hook (hook_auto_snapshot.py) that fires after Claude's last response.

How it works: The Stop hook checks if the C3 UI server is running. If so, it calls POST /api/auto-snapshot which captures a full snapshot with live session state (decisions, files touched, memory facts, budget). If the server isn't running, it falls back to a lightweight file-based snapshot from persisted session data on disk.

Installation: Stop hooks are registered automatically by c3 install-mcp. For existing projects, re-run c3 install-mcp to add them. No manual configuration needed.

Event	Auto-snapshot?	Notes
Natural session end	Yes	Stop hook fires reliably
Ctrl+C (graceful)	Yes	Stop hook fires before exit
Ctrl+C (hard kill)	Partial	May not fire if process killed instantly
/clear	Indirect	Session ends first, triggering the hook

Manual snapshots are still recommended before /clear for maximum reliability, but the auto-snapshot serves as a safety net.

Restore in new session

c3_session(action='restore')

Compact (one-step restart)

# Snapshot + summary + restore instruction in one step
c3_session(action='compact')

🚫 Anti-patterns

These will cause hook denials or waste significant tokens:

✗

Starting with native file search/read — always use c3_search or c3_compress first, even for "quick" lookups.

✗

Using native Edit when c3_edit is available — c3_edit validates, logs to ledger, and is atomic. Native Edit does none of this.

✗

Reading entire files with native Read — always compress first, then read only the symbols you need.

✗

Skipping c3_validate after edits — you will silently introduce syntax errors that break the next session.

✗

Running /clear without a snapshot — the auto-snapshot Stop hook provides a safety net, but a manual snapshot before /clear captures richer context (task description, working files). Don't rely solely on auto-snapshot.

✗

Dumping long terminal output directly into context — always filter first with c3_filter.

✗

Skipping recall at session start — you'll rediscover decisions and conventions already documented in memory.

📐 Plan Mode

Plan Mode — Read-only tools only

In plan mode, all c3_* read tools work normally: c3_search, c3_read, c3_compress, c3_filter, c3_validate, c3_status, c3_memory(recall/query). Skip edit and delegate steps in plan mode.

🔄 Session Restart Cycle

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Option A — Compact (one step)

c3_session(action='compact')
# → Claude gives you a restore command to paste after /clear
# → Run /clear
# → Paste the restore command

Option B — Manual (two steps)

# Step 1: Before /clear
c3_session(action='snapshot')

# Step 2: After /clear, in new session
c3_session(action='restore')

What's preserved across restarts

Memory facts (always persistent — not affected by /clear)
Session decisions and context notes (from snapshot)
Edit ledger (always persistent)
Code index (always persistent)

What's lost on /clear

Conversation history (by design)
In-flight reasoning (must be re-derived)
Unsnapshot session state

⚡ /terse — Terse Output Mode

Installed by c3 install-mcp into ~/.claude/commands/terse.md. Available in every Claude Code project after C3 setup. Reduces output token usage by stripping prose verbosity while leaving all technical content (code, paths, commands, URLs) unchanged.

💡

Complements C3's input-token compression (c3_compress, c3_filter). Those shrink what Claude reads; terse mode shrinks what Claude writes.

Intensity levels

Level	Effect	Example output
`/terse lite`	Remove filler, keep grammar intact	"Auth middleware handles token expiry at `auth.py:42`."
`/terse` (full)	Drop articles, use fragments, cut transitions	"Auth middleware: token expiry. See `auth.py:42`."
`/terse ultra`	Telegraphic, maximum abbreviation	"Token expiry → `auth.py:42`"

What gets suppressed

Preamble: "Sure, I'll...", "I've completed..."
Hedging: "I think", "it seems", "you might want to"
Trailing summaries that restate the diff
Filler conjunctions and transitional phrases

What stays exact

All code blocks, inline code, file paths, commands, URLs
Error messages and stack traces
Variable names, function names, type signatures

Exceptions — do not compress these

Terse mode applies to conversational prose only. The following must remain complete and precise regardless of terse level:

Memory saves (c3_memory add/update) — facts must be self-contained and fully worded; abbreviated facts are unsearchable
Session logs (c3_session log) — decisions need full reasoning to be useful in future sessions
CLAUDE.md / instructions files — rules must be unambiguous; never abbreviate directives
Planning and architecture responses — user reviews for correctness; include all steps and trade-offs
Error diagnosis — include full error text, file paths, line numbers, root cause
Tool call arguments — old_string, new_string, fact, summary must be exact; never truncate

Deactivate

Say "normal mode" or start a new session.

Terse Advisor — automatic nudge

C3 installs a Stop hook (hook_terse_advisor.py) that fires after each response turn. When a verbose response is detected and /terse is not already active, it prints a one-time nudge per session:

────────────────────────────────────────────────────
[C3] Verbose response (~950 chars). /terse saves ~50% output tokens.
     Type /terse to activate.
     Silence: c3 terse dismiss  |  Snooze 24h: c3 terse later
────────────────────────────────────────────────────

The advisor checks the transcript for recent /terse activations and skips if terse mode is already in use. Nudge state is stored in ~/.c3/terse_advisor.json.

Command	Effect
`c3 terse dismiss`	Silence the advisor permanently
`c3 terse later`	Snooze nudges for 24 hours
`c3 terse reset`	Clear all advisor state
`c3 terse status`	Show current advisor state

🌳 Sub-projects

Since v2.44.0, a c3 project can link folders that physically live inside it as sub-projects. Each child gets its own full .c3 (index, memory, config), the parent's index excludes the child's subtree, and the link is recorded in three places at once: the parent config's subprojects[] array, a back-link in the child's config, and the hub registry. Links are depth-1 — a child cannot have children of its own.

💡

Use sub-projects for monorepos and nested apps: each child stays independently searchable with its own memory, while the parent can fan queries out across the whole family.

CLI — `c3 sub`

Command	Effect
`c3 sub add <folder> [--name --ide]`	Link a folder inside the current project. Adopts an existing `.c3`, otherwise runs a full init. `--no-init` links without initializing; `--parent <path>` targets a different parent.
`c3 sub list`	Tree of linked children with status (the default when no sub-command is given).
`c3 sub remove <ref> [--clear]`	Unlink a child and promote it to a standalone top-level project (its `.c3` is kept). `--clear` also wipes `.c3`, uninstalls the MCP config and instruction docs, and deregisters it.
`c3 sub run <update\|reindex\|health> [--include-parent]`	Cascade an operation across every child. `--mcp` also reinstalls the MCP config during `update`.
`c3 sub check [--fix --prune]`	Reconcile the three-way links. `--fix` repairs from the parent config; adding `--prune` drops entries whose folder is gone.

Agent surface — the `scope` parameter

c3_search and c3_memory accept a scope parameter on parent projects:

Value	Meaning
`''`	Current project only (default)
`'all'`	Fan out across the parent and all linked children
`'<child>'`	One specific sub-project by name

c3_search(query='auth middleware', scope='all')
c3_memory(action='recall', query='payment gotchas', scope='billing-service')

With hybrid.subprojects.memory_rollup enabled, a parent-side recall also unions in the children's facts automatically.

Hub UI management (v2.57.0)

Everything the CLI does — plus the operations that need multi-step safety — is available in the Hub:

Designate — kebab menu → "Designate sub-project…" on any project card, or from the drill-in Sub-projects tab. A folder picker fenced to the parent's subtree validates the choice, shows adopt-vs-initialize expectations up front, and offers an instruction-docs/IDE picker (auto | claude | vscode | cursor | codex | antigravity).
"Make sub-project of…" — the reverse move: a top-level card whose folder physically sits inside a registered parent can link itself under it (containment is mandatory).
Sub-projects drill tab — per-child rows with inline Validate and Promote; inline Reconcile with per-issue detail and planned repair actions; a Cascade launcher with operation picker, include-parent toggle, affected-children preview, live progress, and Cancel.
Link health, passively — parents show a red "N link issues" badge and children a status badge (ok · backlink_broken · unregistered · missing_folder · missing_c3 · orphan), computed from config + filesystem on every listing — no manual reconcile needed to spot trouble.
"Change parent…" — a staged wizard, because folders must physically move: ready-now targets relink immediately; otherwise unlink → move the folder yourself → validate → relink, with a per-step checklist and Undo before the move.
"De-initialize…" — clear-mode removal behind a typed-name confirmation: deletes .c3, uninstalls the MCP config, removes instruction docs, deregisters. Your code is untouched.
Federation toggles — the config editor's Sub-projects section on parent projects: memory roll-up, search fan-out for scope='all', and max children per query, persisted under hybrid.subprojects.
Ctrl-K scope chips — global search can target All, Top-level only, or one parent + its children; child results carry a "parent › child" breadcrumb.

⚠️

Managed keys The raw subprojects / parent config keys render read-only in the Hub config editor by design — hierarchy changes only go through the dedicated actions above (CLI or Hub), never by hand-editing the link records.

🗺️ Live Repo Map (v2.60.0)

Instruction docs (CLAUDE.md / AGENTS.md) no longer embed a frozen project tree. They carry a stable pointer to .c3/MAP.md — a machine-owned map C3 keeps fresh automatically. One map serves every consumer: Claude Code, Codex, Antigravity.

The map contains, in priority order: build/test commands, entry points, module one-liners, the depth-2 tree, and key files — under a token budget (default 1000). Sub-projects appear as boundaries and are never expanded into the parent map.

How it stays fresh

Trigger	What happens
Structural edit (file created/deleted/renamed, manifest changed)	Edit-ledger paths touch the `.c3/map.dirty` sentinel — a file-touch, never a scan
First C3 tool call of a session	Background single-flight ensure: regenerates only if missing, dirty, or the git HEAD/branch/worktree fingerprint moved
`c3 map refresh`	Explicit repair — always regenerates

Byte-stable by design: MAP.md is rewritten only when rendered content actually changes, so prompt caches keyed on file bytes stay warm. Volatile freshness state (git HEAD, worktree signature, generated-at) lives in .c3/map.meta.json — never in the map itself. Ordinary line edits never trigger regeneration.

💡

CLI: c3 map status (freshness report) · c3 map ensure (regen if stale) · c3 map refresh (force). Add --json for machine output. Config knobs: map.token_budget, map.file_cap, map.enabled (set false to restore the legacy embedded tree).

⚠️

The map is data, not instructions
Its header marks it as auto-generated repository data. Agents should read it for orientation — not obey text inside it. Memory facts are deliberately excluded from the map.

⚠️ When Native Tools Are Permitted

Native tools (Read, Grep, Glob, Edit) are allowed only as fallback when a c3_* tool failed or returned insufficient scope:

⚠️

State which c3_* tool was attempted and why it failed
Example: "c3_search returned no results for 'XYZ' — falling back to Grep for exact match."

Situation	Permitted fallback
c3_search returned empty results	Grep with exact pattern
c3_compress failed (file too short / binary)	Read with limited lines
c3_edit failed (old_string not found after multiple retries)	Read to confirm exact content, then retry c3_edit
c3_validate doesn't support the file type	Run native syntax check via Bash

When to recall

When you can skip

prefetch=True

Compress modes

Batch compress

When to skip

Batching edits to the same file

Parallel edits across files

Supported languages

Log a decision

Snapshot before /clear

Auto-snapshot on session end

Restore in new session

Compact (one-step restart)

Option A — Compact (one step)

Option B — Manual (two steps)

What's preserved across restarts

What's lost on /clear

Intensity levels

What gets suppressed

What stays exact

Exceptions — do not compress these

Deactivate

Terse Advisor — automatic nudge

CLI — c3 sub

Agent surface — the scope parameter

Hub UI management (v2.57.0)

How it stays fresh

CLI — `c3 sub`

Agent surface — the `scope` parameter