docs(cli): document all commands and exposed tools

Author: yanekyuk

README.md

@@ -35,6 +35,57 @@ Words you will see elsewhere in this doc: **network** = a community you are in;
 
 ## Commands
 
+### Command reference
+
+Every exposed CLI command is listed below. Add `--json` for machine-readable
+results; `conversation stream --json` emits one event per line. Command-specific
+flags are listed in [Options](#options), and examples follow this reference.
+
+| Command | Function |
+| --- | --- |
+| `index help` | Show global help; also available as `index`, `index --help`, or `index -h`. |
+| `index version` | Show the installed version; also available as `index --version` or `index -v`. |
+| `index login` | Sign in through the browser and store this device's session. |
+| `index logout` | Revoke and clear the stored device session. |
+| `index tool list` | List the API's protocol functions, descriptions, and input schemas. |
+| `index tool call <name> --query '<json object>'` | Invoke any function in the [protocol tool reference](#protocol-tool-reference). |
+| `index agent me` | Read the agent selected to handle your negotiations. |
+| `index profile` | Show your own profile. |
+| `index profile show <user-id>` | Show another user's accessible profile. |
+| `index profile sync` | Research public profile information and return a suggested profile without persisting it. |
+| `index intent list` | List signals, with optional archived and result-limit filters. |
+| `index intent show <id>` | Show one signal. |
+| `index intent create <text>` | Create a signal from its description. |
+| `index intent update <id> <text>` | Update and reprocess a signal's description. |
+| `index intent archive <id>` | Archive a signal so it stops participating in discovery. |
+| `index intent add-to-network <id> <network-id>` | Share a signal in a network. |
+| `index intent remove-from-network <id> <network-id>` | Stop sharing a signal in a network. |
+| `index negotiation list` | List negotiations, optionally filtered by intent or open/settled state. |
+| `index negotiation show <opportunity-id>` | Read the negotiation's turns, current state, and available actions. |
+| `index negotiation turn <opportunity-id> --action <action> --message <text> --expected-turn-count <n>` | Submit one `propose`, `counter`, `accept`, or `decline` turn against the observed turn count. |
+| `index opportunity list` | List persisted opportunities, with optional status and result-limit filters. |
+| `index opportunity show <id>` | Show an opportunity's presentation and participants. |
+| `index opportunity accept <id>` | Request acceptance through the server's owner-approval flow. |
+| `index opportunity reject <id>` | Reject an opportunity. |
+| `index network list` | List your networks. |
+| `index network create <title>` | Create a network when eligible, or submit an early-access creation request. |
+| `index network show <id>` | Show a network and its members. |
+| `index network update <id> --title <text>` | Change a network's title. |
+| `index network delete <id>` | Delete a network you own. |
+| `index network join <id>` | Join an open network. |
+| `index network leave <id>` | Leave a network. |
+| `index network invite <id> <email>` | Invite a member by email. |
+| `index conversation list` | List your conversations. |
+| `index conversation with <user-id>` | Open or resume a human DM. |
+| `index conversation show <id>` | Read messages; use `agent --intent-id <id>` for the personal agent's scoped messages and pending question. |
+| `index conversation send <id> <text>` | Send a message; for `agent`, supply `--intent-id` and the displayed `--question-id` when answering a question. |
+| `index conversation stream` | Subscribe to conversation, negotiation, opportunity, and intent events over SSE. |
+| `index conversation help` | Show conversation-specific help. |
+| `index onboarding confirm-profile` | Confirm that the owner has reviewed their profile. |
+| `index onboarding complete` | Complete onboarding once profile confirmation and first-signal prerequisites are met. |
+| `index scrape <url>` | Extract text from a URL, optionally guided by an objective. |
+| `index sync` | Read your profile, networks, and signals into `~/.index/context.json`, or stdout with `--json`. |
+
 ### `index login`
 
 Authenticate with Index Network. Opens a browser window that runs the device authorization grant against your existing session (or a fresh login), then hands this machine a session of its own.
@@ -72,6 +123,39 @@ index agent me --json
 Tool discovery includes the actual input schemas. `--query` must be a JSON
 object; tool failures produce a structured error and a nonzero exit status.
 
+#### Protocol tool reference
+
+The API in this release exposes these 20 functions through `index tool call`.
+Run `index tool list --json` against your selected API to read each function's
+current input schema. The API enforces ownership, membership, and permission
+checks when a function is invoked.
+
+| Function | Purpose |
+| --- | --- |
+| `research_profile` | Research public identity information and return a suggested profile without persisting it. |
+| `read_intents` | Read accessible signals with user, network, and pagination filters. |
+| `create_intent` | Create a signal and link it to the explicitly supplied networks. |
+| `update_intent` | Revise and reprocess a signal's description. |
+| `delete_intent` | Archive a signal. |
+| `add_intent_to_network` | Share a signal in a network. |
+| `list_intent_networks` | List the networks a signal is shared in. |
+| `remove_intent_from_network` | Remove a signal's link to a network. |
+| `search_intents` | Search accessible signals by semantic similarity. |
+| `read_networks` | Read accessible networks and their details. |
+| `read_network_memberships` | Read network memberships and member information. |
+| `update_network` | Update a network's settings. |
+| `create_network` | Create a network, subject to the API's creation permissions. |
+| `delete_network` | Delete a network you own. |
+| `create_network_membership` | Join an open network or add a member when authorized. |
+| `delete_network_membership` | Remove a member from a network you own. |
+| `list_opportunities` | Read persisted opportunities and their presentation. |
+| `update_opportunity` | Request an opportunity status transition under the server's lifecycle rules. |
+| `scrape_url` | Extract text from a URL with an optional objective. |
+| `read_docs` | Read canonical protocol guidance, optionally narrowed to a topic. |
+
+Agent identity, negotiation turns, conversations, and onboarding use their
+dedicated commands above and the corresponding REST endpoints.
+
 ### `index logout`
 
 Revoke this machine's session server-side, then clear the local credential file. A session can revoke itself, so sign-out takes effect immediately without needing your browser. If the server cannot be reached the local file is still cleared, and logout tells you to revoke the device in Index web settings. If local cleanup fails, logout exits nonzero and asks you to remove the file manually.
@@ -236,10 +320,17 @@ index opportunity reject <id>
 | `--app-url <url>`    |       | Override app URL for login (default: `https://index.network`)   |
 | `--archived`         |       | Include archived signals (intent list)                          |
 | `--status <status>`  |       | Filter opportunities by status                                  |
-| `--limit <n>`        |       | Limit number of results                                         |
+| `--limit <n>`        |       | Positive result limit for intent/opportunity lists or conversation messages |
 | `--prompt <text>`    | `-p`  | Network description (for `network create`)                      |
 | `--title <text>`     |       | Network title (for `network update`)                            |
 | `--objective <text>` |       | Focus objective (for `scrape`)                                  |
+| `--query <json>`     |       | Required JSON object for `tool call`                            |
+| `--intent-id <id>`   |       | Filter negotiations, scope agent conversations, or select onboarding's first signal |
+| `--state <state>`    |       | Filter negotiations by `open` or `settled`                       |
+| `--action <action>`  |       | Required negotiation turn action: `propose`, `counter`, `accept`, or `decline` |
+| `--message <text>`   |       | Required message for a negotiation turn                         |
+| `--expected-turn-count <n>` | | Required observed nonnegative integer turn count for a negotiation turn |
+| `--question-id <id>` |       | Identify the displayed question when answering the personal agent |
 | `--json`             |       | Output raw JSON to stdout                                       |
 | `--help`             | `-h`  | Show help                                                       |
 | `--version`          | `-v`  | Show version                                                    |