Update README and docs content

Add new docs pages and LLM context files, and remove the legacy SHANNON-PRO.md file.

docs/workspaces.md

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+# Workspaces and Resuming
+
+Shannon Lite uses workspaces to store scan state, logs, prompts, and deliverables. Workspaces allow interrupted or failed runs to resume without re-running completed agents.
+
+## How Workspaces Work
+
+- Every run creates a workspace.
+- Auto-named workspaces use the target hostname and a session ID, such as `example-com_shannon-1771007534808`.
+- `npx` mode stores workspaces in `~/.shannon/workspaces/`.
+- Source-build mode stores workspaces in `./workspaces/`.
+- Use `-w <name>` to give a run a custom name.
+- To resume a run, pass the same workspace name with `-w`.
+- Each agent's progress is checkpointed so resumed runs can skip completed work.
+
+> [!NOTE]
+> The URL must match the original workspace URL when resuming. Shannon Lite rejects mismatched URLs to prevent cross-target contamination.
+
+## Examples
+
+Start with a named workspace:
+
+```bash
+npx @keygraph/shannon start -u https://example.com -r /path/to/repo -w my-audit
+```
+
+Resume the same workspace:
+
+```bash
+npx @keygraph/shannon start -u https://example.com -r /path/to/repo -w my-audit
+```
+
+Resume an auto-named workspace:
+
+```bash
+npx @keygraph/shannon start -u https://example.com -r /path/to/repo -w example-com_shannon-1771007534808
+```
+
+List all workspaces:
+
+```bash
+npx @keygraph/shannon workspaces
+```
+
+Source-build equivalents:
+
+```bash
+./shannon start -u https://example.com -r /path/to/repo -w my-audit
+./shannon start -u https://example.com -r /path/to/repo -w example-com_shannon-1771007534808
+./shannon workspaces
+```