feat: Clean up root directory and create docs folder

This reverts commit 33e9a861b0.

docs/JENKINS-FINDINGS.md

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+# Jenkins Cloudron Package - Findings and Research
+
+## Phase 1, Step 1: Review Existing Jenkins Package - Findings:
+
+The directory `CloudronPackages/Jenkins/` contains the following files and directories:
+*   `casc_templates/` (directory)
+*   `CloudronManifest.json`
+*   `Dockerfile`
+*   `JenkinsBulldNotes.md` (Note: There's a typo in the filename, "BulldNotes" instead of "BuildNotes". This will be corrected later.)
+*   `nginx.conf`
+*   `start.sh`
+*   `supervisor.conf`
+
+This confirms that a partial Jenkins package already exists, providing a good starting point.
+
+## Phase 1, Step 2: Research Jenkins Requirements - Findings from Existing Files and Initial Research:
+
+### `CloudronManifest.json`:
+*   `id`: `io.jenkins.cloudron`
+*   `title`: `Jenkins`
+*   `author`: `Cloudron Packager`
+*   `description`: `Jenkins is an open source automation server which enables developers to reliably build, test, and deploy their software.`
+*   `tagline`: `The leading open source automation server`
+*   `version`: `1.0.0` (This is likely outdated, Jenkins has much higher versions and should be updated to reflect the actual Jenkins version installed).
+*   `healthCheckPath`: `/login` (This is a good starting point).
+*   `httpPort`: `8080` (Standard Jenkins port).
+*   `manifestVersion`: `2`
+*   `website`: `https://jenkins.io/`
+*   `contactEmail`: `support@cloudron.io`
+*   `icon`: `file://logo.png` (The `logo.png` file is not present in the `CloudronPackages/Jenkins/` directory and will need to be added).
+*   `dockerImage`: `cloudron/jenkins` (This is the image name *this* package will produce, not the base image).
+*   `memoryLimit`: `2048000000` (2GB, seems reasonable for a start).
+*   `addons`: `localstorage` (for `/app/data`).
+*   `optionalAddons`: `ldap`, `oauth` (suggests integration with Cloudron's authentication).
+*   `tags`: `ci`, `cd`, `devops`, `automation`
+*   `postInstallMessage`: Provides instructions for initial admin password.
+*   `minBoxVersion`: `5.4.0`.
+*   `documentationUrl`: `https://jenkins.io/doc/`
+
+### `Dockerfile`:
+*   `FROM cloudron/base:4.2.0` (Good, standard Cloudron base image).
+*   Installs `openjdk-17-jdk` (Jenkins requires Java. Need to confirm if this is the recommended Java version for the latest stable Jenkins).
+*   Adds Jenkins repository key and repository (`https://pkg.jenkins.io/debian-stable`).
+*   Installs `jenkins` package.
+*   Installs specific Jenkins plugins (`ldap.hpi`, `oic-auth.hpi`, `configuration-as-code.hpi`, `credentials.hpi`) by curling them from `updates.jenkins.io`. (It might be better to use the Jenkins CLI to install plugins during the build process, which can handle dependencies and ensure compatibility).
+*   Copies `casc_templates/` to `/tmp/data/casc_configs/`.
+*   Sets up `/app/data` and `/tmp/data/jenkins_home`.
+*   Copies `start.sh`, `nginx.conf`, `supervisor.conf`.
+*   `usermod -a -G jenkins cloudron && chown -R cloudron:cloudron /tmp/data` (This is crucial for permissions).
+*   `WORKDIR /app/data`.
+*   `CMD ["/app/code/start.sh"]`.
+
+### `start.sh`:
+*   Sets `JENKINS_HOME=/app/data/jenkins_home`.
+*   Initializes `JENKINS_HOME` by copying from `/tmp/data/jenkins_home` and plugins from `/tmp/data/plugins`.
+*   Sets permissions with `chown -R cloudron:cloudron "${JENKINS_HOME}"`.
+*   Sets `JENKINS_OPTS` and `JAVA_OPTS` to disable setup wizard.
+*   Uses `CLOUDRON_OAUTH_CLIENT_ID` and `CLOUDRON_LDAP_SERVER` to determine which JCasC (`casc_templates`) configuration to use (`oauth.yaml`, `ldap.yaml`, or `default.yaml`).
+*   Configures `JENKINS_URL` using `CLOUDRON_APP_ORIGIN`.
+*   `exec /usr/bin/supervisord --nodaemon -c /etc/supervisor/supervisord.conf` (Jenkins is managed by Supervisor, along with Nginx).
+
+### `JenkinsBulldNotes.md`:
+*   Confirms the file structure and purpose of each file.
+*   Provides build and test instructions using `cloudron build` and `cloudron install`.
+*   Details authentication configuration via JCasC and Cloudron addons.
+*   Outlines testing steps (basic functionality, authentication, persistence).
+*   Mentions `jenkins_home` is persisted in `/app/data/jenkins_home`.
+*   Notes initial admin password is `adminpass` (this is likely set in `default.yaml` in `casc_templates`).
+
+## Overall Assessment:
+
+The existing Jenkins package is quite comprehensive and seems to follow Cloudron conventions well. It includes support for different authentication methods via JCasC, which is a good practice. The use of `supervisor` to manage Jenkins and Nginx is also standard for Cloudron packages.
+
+## Key areas for further research/consideration:
+
+*   **Jenkins Version**: The `Dockerfile` installs Jenkins from `pkg.jenkins.io/debian-stable`. This will install the latest stable version available in that repository. The `CloudronManifest.json` has `version: "1.0.0"`, which is a placeholder and should be updated to reflect the actual Jenkins version installed.
+*   **Java Version**: The Dockerfile installs `openjdk-17-jdk`. I should confirm if this is the recommended Java version for the latest stable Jenkins.
+*   **Plugins**: The Dockerfile curls specific plugin versions. It might be better to use the Jenkins CLI to install plugins during the build process, which can handle dependencies and ensure compatibility.
+*   **`logo.png`**: The `CloudronManifest.json` references `icon: "file://logo.png"`, but `logo.png` is not present in the `CloudronPackages/Jenkins/` directory. I will need to add a suitable logo.
+*   **`JenkinsBulldNotes.md` Typo**: I will correct the typo in the filename to `JenkinsBuildNotes.md`.

docs/LEARNING.md

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+# Learning Log - Gemini CLI
+
+This document records mistakes made during interactions and their corresponding solutions, aiming to improve future performance and accuracy.
+
+## Docker and File Operation Mistakes
+
+### 1. `config.yaml` not found during Docker build
+- **Mistake**: Assumed `config.yaml` would be present for `COPY` instruction in Dockerfile when it was dynamically generated by `start.sh` at runtime.
+- **Solution**: Created a placeholder `config.yaml` file in the build context to satisfy the `COPY` instruction during the Docker build process. The `start.sh` script then overwrites this placeholder with the dynamically generated content.
+
+### 2. `apt-get` permission denied during Docker build
+- **Mistake**: Encountered `E: Could not open lock file /var/lib/apt/lists/lock - open (13: Permission denied)` during `apt-get update` or `install` in Dockerfile.
+- **Solution**: Explicitly set `USER root` before `apt-get` commands in the Dockerfile to ensure they run with necessary privileges. Also, ensured `DEBIAN_FRONTEND=noninteractive` was used to prevent interactive prompts.
+
+### 3. `chown: invalid user: 'cloudron:cloudron'`
+- **Mistake**: Attempted to change ownership of files to `cloudron:cloudron` before the `cloudron` user and group were created in the Docker image.
+- **Solution**: Added explicit `RUN groupadd -r cloudron && useradd -r -g cloudron cloudron` commands in the Dockerfile *before* the `chown` instruction to ensure the user and group exist.
+
+### 4. `docker run -it` "the input device is not a TTY"
+- **Mistake**: Attempted to run Docker containers with `-it` flags in a non-interactive environment, leading to TTY errors.
+- **Solution**: For running containers in the background, use detached mode (`-d`) and rely on `docker logs` or `docker cp` for inspecting output and files. Avoid `-it` unless a true interactive terminal session is required and supported by the environment.
+
+### 5. `replace` tool "No changes to apply" or "Expected 1 occurrence but found X"
+- **Mistake**: Provided `old_string` to the `replace` tool that either did not exactly match the target text or matched multiple times, leading to failed or unintended operations.
+- **Solution**: Always read the file content immediately before using `replace` to obtain the *exact* `old_string` (including all whitespace, indentation, and line endings). For complex blocks or when multiple matches are a risk, consider overwriting the entire file content using `write_file` if appropriate for the context.
+
+### 6. `start.sh` duplication
+- **Mistake**: Unintended duplication of script content within `start.sh` due to imprecise `replace` operations, where a section of the script was inadvertently appended to itself.
+- **Solution**: When making significant structural changes or large modifications to a script, it is safer and more reliable to read the entire file, perform the modifications in memory, and then overwrite the entire file using `write_file`.
+
+### 7. APISIX etcd connection issues (local testing)
+- **Mistake**: Presumed APISIX would run in a truly standalone mode for local testing without an etcd instance, or that `localhost` would correctly resolve to a host-exposed etcd port from within the container.
+- **Solution**: For local testing of applications with external dependencies like etcd, explicitly spin up the dependent service in a separate container. Connect the application container to the dependency container using a user-defined Docker network and refer to the dependency by its service name (e.g., `apisix-etcd`) as the hostname. This accurately simulates the Cloudron environment where addons are provided as networked services.