feat: add comprehensive documentation for yanpm-agent, including API reference, configuration, deployment, usage examples, and troubleshooting

apps/agent/doc/configuration.md

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+# Configuration and Environment
+
+CLI flags and environment variables
+
+- `--sock` / `YANPM_AGENT_SOCK` (default: `./yanpm-agent.sock`)
+  - Path to the Unix socket file the agent will bind to.
+  - If the socket directory does not exist the agent attempts to create it and set mode `0770`.
+
+- `--nginx-config-dir` / `YANPM_NGINX_CONFIG_DIR` (default: `/etc/nginx/conf.d`)
+  - Directory where nginx fragments are written. The agent writes fragments into a subdirectory named by the agent (internal use).
+
+- `--sock-perm` / `YANPM_AGENT_SOCK_PERM` (default: `660`)
+  - A 3-digit octal permission string applied to the socket file (best-effort). The program validates this is a 3-digit octal string.
+  - If the final digit is greater than `0` a warning is logged because that allows "others" access.
+
+- `--sock-gid` / `YANPM_AGENT_SOCK_GID` (default: current user's primary group)
+  - GID to set on the socket file (best-effort).
+
+Validation rules and behavior
+
+- `sock_perm` must be exactly 3 octal digits (characters 0-7). The agent rejects invalid values at startup.
+- When an existing path exists at the socket location the agent verifies it is a unix socket; if so it removes it before binding. If the path exists and is not a socket, startup fails.
+- Setting permissions (`set_permissions`) and changing GID (`chown`) are attempted but non-fatal: failures are logged as warnings and the agent continues.
+
+Notes about nginx config directory
+
+- The agent writes fragments into a subdirectory (internal) of the configured `nginx_config_dir`. Ensure nginx is configured to include that subdirectory so fragments are picked up, or use `write_config` then trigger a reload.