Config discovery uses process.cwd() instead of ctx.cwd

[adameq]

The extension resolves project config paths from process.cwd() instead of the session's
ctx.cwd. When a session's workspace differs from the process working directory,
.pi/agents/ and .pi/subagents.json are read from the wrong tree — silently.

Every Agent call then falls back to the built-in general-purpose. Because that agent uses
prompt_mode: append, subagents inherit the full parent prompt and the complete tool set, so
tools:, disallowed_tools:, extensions: false and isolated: true are all ignored —
agents authored as read-only get edit/write. The only hint is
Unknown agent type "<name>" — using general-purpose, which reads like a typo, not a path bug.

Call sites (master): src/index.ts 283 (loadCustomAgents), 872
(agent-tool-description.md), 1572-1573 (agent dirs), 750 (applyAndEmitLoaded called
without cwd); src/settings.ts 251, 260, 310, 328 (cwd: string = process.cwd() defaults).
saveSettings shares the default, so settings written from /agents → Settings also land
outside the project.

When the two differ. Not in normal CLI use — running pi inside the project makes
process.cwd() === ctx.cwd, which is presumably why this went unnoticed. The CLI actively
keeps it that way: resuming a session from another directory prompts
Session found in different project — fork into current directory?, and the fork rewrites the
session cwd to the current one. So the divergence is reachable through the SDK
(docs/sdk.md, "embed pi in other applications"): a host process that creates sessions whose
workspace is not the directory the process was started in. That is what I hit.

Repro — pi 0.83.0, extension 0.14.3, node 24.18.0, Linux.

1. Project at /home/me/project containing .pi/agents/my-agent.md and .pi/subagents.json
2. Embed pi via the SDK and open a session with that project as its workspace, from a process
   whose own cwd is elsewhere (e.g. $HOME)
3. Confirm the workspace is correct — bash pwd, git branch and file listing all report the project
4. Call Agent({ subagent_type: "my-agent", ... })

Actual: Unknown agent type "my-agent" — using general-purpose; .pi/subagents.json is
ignored as well (maxConcurrent, outputTranscript, toolDescriptionMode fall back to defaults).
Expected: the agent from .pi/agents/ is used and project settings apply.

Fix direction: ctx.cwd is already used throughout the same file (resolveStorePath,
createOutputFilePath, readEnabledModels), and the SDK documents this pattern for project
config — docs/extensions.md:958-962 shows
pi.on("session_start", (_event, ctx) => join(ctx.cwd, CONFIG_DIR_NAME, "my-extension.json")).
reloadCustomAgents() has 15 call sites and all but the init one at index.ts:288 have ctx
in scope, so threading cwd through is mostly mechanical.

I fixed the same bug in two extensions of my own, and after the change they work correctly in
the very same host process that still breaks this one — so a one-sided fix here is sufficient.

Happy to open a PR if you want it.