feat: Phase 2 — project registry, legacy field cleanup, credential path fix

- task.Project type + storage CRUD + UpsertProject + SeedProjects
- Remove AgentConfig.ProjectDir, RepositoryURL, SkipPlanning
- Remove ContainerRunner fallback git init logic
- Project API endpoints: GET/POST /api/projects, GET/PUT /api/projects/{id}
- processResult no longer extracts changestats (pool-side only)
- claude_config_dir config field; default to credentials/claude/
- New scripts: sync-credentials, fix-permissions, check-token

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

1 files changed, 43 insertions, 0 deletions

diff --git a/scripts/fix-permissions b/scripts/fix-permissions
new file mode 100644
index 0000000..408a23e
--- /dev/null
+++ b/scripts/fix-permissions
@@ -0,0 +1,43 @@
+#!/bin/bash
+# claudomator-fix-perms — Fix ownership and permissions for Claudomator components
+set -euo pipefail
+
+SITE_DIR="/site/doot.terst.org"
+GIT_REPOS_DIR="/site/git.terst.org/repos"
+WORKSPACE_DIR="/workspace"
+
+echo "==> Fixing site ownership (www-data:www-data)..."
+chown -R www-data:www-data "${SITE_DIR}"
+
+echo "==> Ensuring binaries are executable..."
+if [ -d "${SITE_DIR}/bin" ]; then
+    find "${SITE_DIR}/bin" -type f -exec chmod +x {} +
+fi
+if [ -f "/usr/local/bin/claudomator" ]; then
+    chmod +x /usr/local/bin/claudomator
+fi
+
+echo "==> Ensuring scripts are executable..."
+if [ -d "${SITE_DIR}/scripts" ]; then
+    find "${SITE_DIR}/scripts" -type f -exec chmod +x {} +
+fi
+if [ -d "${WORKSPACE_DIR}/claudomator/scripts" ]; then
+    find "${WORKSPACE_DIR}/claudomator/scripts" -type f -exec chmod +x {} +
+fi
+
+echo "==> Fixing git bare repo permissions..."
+# Specifically fix object permissions that might be corrupted by root runs
+if [ -d "${GIT_REPOS_DIR}" ]; then
+    chown -R www-data:www-data "${GIT_REPOS_DIR}"
+    find "${GIT_REPOS_DIR}" -type d -exec chmod 775 {} +
+    find "${GIT_REPOS_DIR}" -type f -exec chmod 664 {} +
+fi
+
+echo "==> Fixing database permissions..."
+if [ -f "${SITE_DIR}/data/claudomator.db" ]; then
+    chmod 664 "${SITE_DIR}/data/claudomator.db"
+    # Ensure the data directory is writable for WAL mode
+    chmod 775 "${SITE_DIR}/data"
+fi
+
+echo "==> Done!"