20 files changed, 286 insertions, 32 deletions
diff --git a/doc/book/build/_index.md b/doc/book/build/_index.md
index 9bb17086..021045aa 100644
--- a/doc/book/build/_index.md
+++ b/doc/book/build/_index.md
@@ -1,6 +1,6 @@
 +++
 title = "Build your own app"
-weight = 4
+weight = 40
 sort_by = "weight"
 template = "documentation.html"
 +++
diff --git a/doc/book/connect/_index.md b/doc/book/connect/_index.md
index 93a2b87e..7d8e686c 100644
--- a/doc/book/connect/_index.md
+++ b/doc/book/connect/_index.md
@@ -1,6 +1,6 @@
 +++
 title = "Existing integrations"
-weight = 3
+weight = 30
 sort_by = "weight"
 template = "documentation.html"
 +++
diff --git a/doc/book/cookbook/_index.md b/doc/book/cookbook/_index.md
index 07bf6ebf..ff90ad52 100644
--- a/doc/book/cookbook/_index.md
+++ b/doc/book/cookbook/_index.md
@@ -1,7 +1,7 @@
 +++
 title="Cookbook"
 template = "documentation.html"
-weight = 2
+weight = 20
 sort_by = "weight"
 +++
 
@@ -37,7 +37,3 @@ This chapter could also be referred as "Tutorials" or "Best practices".
 - **[Monitoring Garage](@/documentation/cookbook/monitoring.md)** This page
   explains the Prometheus metrics available for monitoring the Garage
   cluster/nodes.
-
-- **[Recovering from failures](@/documentation/cookbook/recovering.md):** Garage's first selling point is resilience
-  to hardware failures. This section explains how to recover from such a failure in the
-  best possible way.
diff --git a/doc/book/cookbook/encryption.md b/doc/book/cookbook/encryption.md
new file mode 100644
index 00000000..8d45a0ee
--- /dev/null
+++ b/doc/book/cookbook/encryption.md
@@ -0,0 +1,108 @@
++++
+title = "Encryption"
+weight = 50
++++
+
+Encryption is a recurring subject when discussing Garage. 
+Garage does not handle data encryption by itself, but many things can
+already be done with Garage's current feature set and the existing ecosystem.
+
+This page takes a high level approach to security in general and data encryption
+in particular.
+
+
+# Examining your need for encryption
+
+- Why do you want encryption in Garage?
+
+- What is your threat model? What are you fearing?
+  - A stolen HDD?
+  - A curious administrator?
+  - A malicious administrator?
+  - A remote attacker?
+  - etc.
+
+- What services do you want to protect with encryption?
+  - An existing application? Which one? (eg. Nextcloud)
+  - An application that you are writing
+
+- Any expertise you may have on the subject
+
+This page explains what Garage provides, and how you can improve the situation by yourself
+by adding encryption at different levels.
+
+We would be very curious to know your needs and thougs about ideas such as
+encryption practices and things like key management, as we want Garage to be a
+serious base platform for the developpment of secure, encrypted applications.
+Do not hesitate to come talk to us if you have any thoughts or questions on the
+subject.
+
+
+# Capabilities provided by Garage
+
+## Traffic is encrypted between Garage nodes
+
+RPCs between Garage nodes are encrypted. More specifically, contrary to many
+distributed software, it is impossible in Garage to have clear-text RPC.  We
+use the [kuska handshake](https://github.com/Kuska-ssb/handshake) library which
+implements a protocol that has been clearly reviewed, Secure ScuttleButt's
+Secret Handshake protocol.  This is why setting a `rpc_secret` is mandatory,
+and that's also why your nodes have super long identifiers.
+
+## HTTP API endpoints provided by Garage are in clear text
+
+Adding TLS support built into Garage is not currently planned.
+
+## Garage stores data in plain text on the filesystem
+
+Garage does not handle data encryption at rest by itself, and instead delegates
+to the user to add encryption, either at the storage layer (LUKS, etc) or on
+the client side (or both). There are no current plans to add data encryption
+directly in Garage.
+
+Implementing data encryption directly in Garage might make things simpler for
+end users, but also raises many more questions, especially around key
+management: for encryption of data, where could Garage get the encryption keys
+from ? If we encrypt data but keep the keys in a plaintext file next to them,
+it's useless. We probably don't want to have to manage secrets in garage as it
+would be very hard to do in a secure way. Maybe integrate with an external
+system such as Hashicorp Vault?
+
+
+# Adding data encryption using external tools
+
+## Encrypting traffic between a Garage node and your client
+
+You have multiple options to have encryption between your client and a node:
+
+  - Setup a reverse proxy with TLS / ACME / Let's encrypt
+  - Setup a Garage gateway locally, and only contact the garage daemon on `localhost`
+  - Only contact your Garage daemon over a secure, encrypted overlay network such as Wireguard
+
+## Encrypting data at rest
+
+Protects against the following threats:
+
+- Stolen HDD
+
+Crucially, does not protect againt malicious sysadmins or remote attackers that
+might gain access to your servers.
+
+Methods include full-disk encryption with tools such as LUKS.
+
+## Encrypting data on the client side
+
+Protects againt the following threats:
+
+- A honest-but-curious administrator
+- A malicious administrator that tries to corrupt your data
+- A remote attacker that can read your server's data
+
+Implementations are very specific to the various applications. Examples:
+
+- Matrix: uses the OLM protocol for E2EE of user messages. Media files stored
+  in Matrix are probably encrypted using symmetric encryption, with a key that is
+  distributed in the end-to-end encrypted message that contains the link to the object.
+
+- Aerogramme: use the user's password as a key to decrypt data in the user's bucket
+
diff --git a/doc/book/cookbook/monitoring.md b/doc/book/cookbook/monitoring.md
index 8313daa9..b204dbbe 100644
--- a/doc/book/cookbook/monitoring.md
+++ b/doc/book/cookbook/monitoring.md
@@ -49,9 +49,5 @@ add the following lines in your Prometheus scrape config:
 To visualize the scraped data in Grafana,
 you can either import our [Grafana dashboard for Garage](https://git.deuxfleurs.fr/Deuxfleurs/garage/raw/branch/main/script/telemetry/grafana-garage-dashboard-prometheus.json)
 or make your own.
-We detail below the list of exposed metrics and their meaning.
 
-
-## List of exported metrics
-
-See our [dedicated page](@/documentation/reference-manual/monitoring.md) in the Reference manual section.
+The list of exported metrics is available on our [dedicated page](@/documentation/reference-manual/monitoring.md) in the Reference manual section.
diff --git a/doc/book/cookbook/real-world.md b/doc/book/cookbook/real-world.md
index 08266b23..7061069f 100644
--- a/doc/book/cookbook/real-world.md
+++ b/doc/book/cookbook/real-world.md
@@ -197,6 +197,12 @@ The `garage` binary has two purposes:
 Ensure an appropriate `garage` binary (the same version as your Docker image) is available in your path.
 If your configuration file is at `/etc/garage.toml`, the `garage` binary should work with no further change.
 
+You can also use an alias as follows to use the Garage binary inside your docker container:
+
+```bash
+alias garage="docker exec -ti <container name> /garage"
+```
+
 You can test your `garage` CLI utility by running a simple command such as:
 
 ```bash
@@ -339,7 +345,7 @@ garage layout apply
 ```
 
 **WARNING:** if you want to use the layout modification commands in a script,
-make sure to read [this page](@/documentation/reference-manual/layout.md) first.
+make sure to read [this page](@/documentation/operations/layout.md) first.
 
 
 ## Using your Garage cluster
diff --git a/doc/book/cookbook/systemd.md b/doc/book/cookbook/systemd.md
index b271010b..c0ed7d1f 100644
--- a/doc/book/cookbook/systemd.md
+++ b/doc/book/cookbook/systemd.md
@@ -33,7 +33,20 @@ NoNewPrivileges=true
 WantedBy=multi-user.target
 ```
 
-*A note on hardening: garage will be run as a non privileged user, its user id is dynamically allocated by systemd. It cannot access (read or write) home folders (/home, /root and /run/user), the rest of the filesystem can only be read but not written, only the path seen as /var/lib/garage is writable as seen by the service (mapped to /var/lib/private/garage on your host). Additionnaly, the process can not gain new privileges over time.*
+**A note on hardening:** Garage will be run as a non privileged user, its user
+id is dynamically allocated by systemd (set with `DynamicUser=true`). It cannot
+access (read or write) home folders (`/home`, `/root` and `/run/user`), the
+rest of the filesystem can only be read but not written, only the path seen as
+`/var/lib/garage` is writable as seen by the service. Additionnaly, the process
+can not gain new privileges over time.
+
+For this to work correctly, your `garage.toml` must be set with
+`metadata_dir=/var/lib/garage/meta` and `data_dir=/var/lib/garage/data`. This
+is mandatory to use the DynamicUser hardening feature of systemd, which
+autocreates these directories as virtual mapping. If the directory
+`/var/lib/garage` already exists before starting the server for the first time,
+the systemd service might not start correctly.  Note that in your host
+filesystem, Garage data will be held in `/var/lib/private/garage`.
 
 To start the service then automatically enable it at boot:
 
diff --git a/doc/book/design/_index.md b/doc/book/design/_index.md
index 50933139..5881ab8f 100644
--- a/doc/book/design/_index.md
+++ b/doc/book/design/_index.md
@@ -1,6 +1,6 @@
 +++
 title = "Design"
-weight = 6
+weight = 70
 sort_by = "weight"
 template = "documentation.html"
 +++
diff --git a/doc/book/design/goals.md b/doc/book/design/goals.md
index 4e390ba6..78ac7978 100644
--- a/doc/book/design/goals.md
+++ b/doc/book/design/goals.md
@@ -42,15 +42,13 @@ locations. They use Garage themselves for the following tasks:
 
 - As a [Matrix media backend](https://github.com/matrix-org/synapse-s3-storage-provider)
 
-- To store personal data and shared documents through [Bagage](https://git.deuxfleurs.fr/Deuxfleurs/bagage), a homegrown WebDav-to-S3 proxy
+- As a Nix binary cache
 
-- In the Drone continuous integration platform to store task logs
+- To store personal data and shared documents through [Bagage](https://git.deuxfleurs.fr/Deuxfleurs/bagage), a homegrown WebDav-to-S3 and SFTP-to-S3 proxy
 
-- As a Nix binary cache
+- As a backup target using `rclone` and `restic`
 
-- As a backup target using `rclone`
+- In the Drone continuous integration platform to store task logs
 
 The Deuxfleurs Garage cluster is a multi-site cluster currently composed of
-4 nodes in 2 physical locations. In the future it will be expanded to at
-least 3 physical locations to fully exploit Garage's potential for high
-availability.
+9 nodes in 3 physical locations.
diff --git a/doc/book/design/internals.md b/doc/book/design/internals.md
index 777e017d..cefb7acc 100644
--- a/doc/book/design/internals.md
+++ b/doc/book/design/internals.md
@@ -61,7 +61,7 @@ Garage prioritizes which nodes to query according to a few criteria:
 
 
 For further reading on the cluster structure look at the [gateway](@/documentation/cookbook/gateways.md) 
-and [cluster layout management](@/documentation/reference-manual/layout.md) pages.
+and [cluster layout management](@/documentation/operations/layout.md) pages.
 
 ## Garbage collection
 
diff --git a/doc/book/development/_index.md b/doc/book/development/_index.md
index 8e730bf6..2b2af0cc 100644
--- a/doc/book/development/_index.md
+++ b/doc/book/development/_index.md
@@ -1,6 +1,6 @@
 +++
 title = "Development"
-weight = 7
+weight = 80
 sort_by = "weight"
 template = "documentation.html"
 +++
diff --git a/doc/book/operations/_index.md b/doc/book/operations/_index.md
new file mode 100644
index 00000000..16d0e9d5
--- /dev/null
+++ b/doc/book/operations/_index.md
@@ -0,0 +1,23 @@
++++
+title = "Operations & Maintenance"
+weight = 50
+sort_by = "weight"
+template = "documentation.html"
++++
+
+This section contains a number of important information on how to best operate a Garage cluster,
+to ensure integrity and availability of your data:
+
+- **[Upgrading Garage](@/documentation/operations/upgrading.md):** General instructions on how to
+  upgrade your cluster from one version to the next. Instructions specific for each version upgrade
+  can bef ound in the [working documents](@/documentation/working-documents/_index.md) section.
+
+- **[Layout management](@/documentation/operations/layout.md):** Best practices for using the `garage layout`
+  commands when adding or removing nodes from your cluster.
+
+- **[Durability and repairs](@/documentation/operations/durability-repairs.md):** How to check for small things
+  that might be going wrong, and how to recover from such failures.
+
+- **[Recovering from failures](@/documentation/operations/recovering.md):** Garage's first selling point is resilience
+  to hardware failures. This section explains how to recover from such a failure in the
+  best possible way.
diff --git a/doc/book/operations/durability-repairs.md b/doc/book/operations/durability-repairs.md
new file mode 100644
index 00000000..b8992f85
--- /dev/null
+++ b/doc/book/operations/durability-repairs.md
@@ -0,0 +1,114 @@
++++
+title = "Durability & Repairs"
+weight = 30
++++
+
+To ensure the best durability of your data and to fix any inconsistencies that may
+pop up in a distributed system, Garage provides a serires of repair operations.
+This guide will explain the meaning of each of them and when they should be applied.
+
+
+# General syntax of repair operations
+
+Repair operations described below are of the form `garage repair <repair_name>`.
+These repairs will not launch without the `--yes` flag, which should
+be added as follows: `garage repair --yes <repair_name>`.
+By default these repair procedures will only run on the Garage node your CLI is
+connecting to. To run on all nodes, add the `-a` flag as follows:
+`garage repair -a --yes <repair_name>`.
+
+# Data block operations
+
+## Data store scrub
+
+Scrubbing the data store means examining each individual data block to check that
+their content is correct, by verifying their hash. Any block found to be corrupted
+(e.g. by bitrot or by an accidental manipulation of the datastore) will be
+restored from another node that holds a valid copy.
+
+A scrub is run automatically by Garage every 30 days. It can also be launched
+manually using `garage repair scrub start`.
+
+To view the status of an ongoing scrub, first find the task ID of the scrub worker
+using `garage worker list`. Then, run `garage worker info <scrub_task_id>` to
+view detailed runtime statistics of the scrub. To gather cluster-wide information,
+this command has to be run on each individual node.
+
+A scrub is a very disk-intensive operation that might slow down your cluster.
+You may pause an ongoing scrub using `garage repair scrub pause`, but note that
+the scrub will resume automatically 24 hours later as Garage will not let your
+cluster run without a regular scrub. If the scrub procedure is too intensive
+for your servers and is slowing down your workload, the recommended solution
+is to increase the "scrub tranquility" using `garage repair scrub set-tranquility`.
+A higher tranquility value will make Garage take longer pauses between two block
+verifications. Of course, scrubbing the entire data store will also take longer.
+
+## Block check and resync
+
+In some cases, nodes hold a reference to a block but do not actually have the block
+stored on disk. Conversely, they may also have on disk blocks that are not referenced
+any more. To fix both cases, a block repair may be run with `garage repair blocks`.
+This will scan the entire block reference counter table to check that the blocks
+exist on disk, and will scan the entire disk store to check that stored blocks
+are referenced.
+
+It is recommended to run this procedure when changing your cluster layout,
+after the metadata tables have finished synchronizing between nodes
+(usually a few hours after `garage layout apply`).
+
+## Inspecting lost blocks
+
+In extremely rare situations, data blocks may be unavailable from the entire cluster.
+This means that even using `garage repair blocks`, some nodes may be unable
+to fetch data blocks for which they hold a reference.
+
+These errors are stored on each node in a list of "block resync errors", i.e.
+blocks for which the last resync operation failed.
+This list can be inspected using `garage block list-errors`.
+These errors usually fall into one of the following categories:
+
+1. a block is still referenced but the object was deleted, this is a case
+   of metadata reference inconsistency (see below for the fix)
+2. a block is referenced by a non-deleted object, but could not be fetched due
+   to a transient error such as a network failure
+3. a block is referenced by a non-deleted object, but could not be fetched due
+   to a permanent error such as there not being any valid copy of the block on the
+   entire cluster
+
+To help make the difference between cases 1 and cases 2 and 3, you may use the
+`garage block info` command to see which objects hold a reference to each block.
+
+In the second case (transient errors), Garage will try to fetch the block again
+after a certain time, so the error should disappear natuarlly. You can also
+request Garage to try to fetch the block immediately using `garage block retry-now`
+if you have fixed the transient issue.
+
+If you are confident that you are in the third scenario and that your data block
+is definitely lost, then there is no other choice than to declare your S3 objects
+as unrecoverable, and to delete them properly from the data store. This can be done
+using the `garage block purge` command.
+
+
+# Metadata operations
+
+## Metadata table resync
+
+Garage automatically resyncs all entries stored in the metadata tables every hour,
+to ensure that all nodes have the most up-to-date version of all the information
+they should be holding.
+The resync procedure is based on a Merkle tree that allows to efficiently find
+differences between nodes.
+
+In some special cases, e.g. before an upgrade, you might want to run a table
+resync manually. This can be done using `garage repair tables`.
+
+## Metadata table reference fixes
+
+In some very rare cases where nodes are unavailable, some references between objects
+are broken. For instance, if an object is deleted, the underlying versions or data
+blocks may still be held by Garage. If you suspect that such corruption has occurred
+in your cluster, you can run one of the following repair procedures:
+
+- `garage repair versions`: checks that all versions belong to a non-deleted object, and purges any orphan version
+- `garage repair block_refs`: checks that all block references belong to a non-deleted object version, and purges any orphan block reference (this will then allow the blocks to be garbage-collected)
+
diff --git a/doc/book/reference-manual/layout.md b/doc/book/operations/layout.md
index a7d6f51f..5e314246 100644
--- a/doc/book/reference-manual/layout.md
+++ b/doc/book/operations/layout.md
@@ -1,6 +1,6 @@
 +++
 title = "Cluster layout management"
-weight = 50
+weight = 20
 +++
 
 The cluster layout in Garage is a table that assigns to each node a role in
diff --git a/doc/book/cookbook/recovering.md b/doc/book/operations/recovering.md
index 2129a7f3..7a830788 100644
--- a/doc/book/cookbook/recovering.md
+++ b/doc/book/operations/recovering.md
@@ -1,6 +1,6 @@
 +++
 title = "Recovering from failures"
-weight = 50
+weight = 40
 +++
 
 Garage is meant to work on old, second-hand hardware.
diff --git a/doc/book/cookbook/upgrading.md b/doc/book/operations/upgrading.md
index 9d60a988..e8919a19 100644
--- a/doc/book/cookbook/upgrading.md
+++ b/doc/book/operations/upgrading.md
@@ -1,6 +1,6 @@
 +++
 title = "Upgrading Garage"
-weight = 60
+weight = 10
 +++
 
 Garage is a stateful clustered application, where all nodes are communicating together and share data structures.
@@ -58,7 +58,7 @@ From a high level perspective, a major upgrade looks like this:
 
 ### Major upgarades with minimal downtime
 
-There is only one operation that has to be coordinated cluster-wide: the passage of one version of the internal RPC protocol to the next.
+There is only one operation that has to be coordinated cluster-wide: the switch of one version of the internal RPC protocol to the next.
 This means that an upgrade with very limited downtime can simply be performed from one major version to the next by restarting all nodes
 simultaneously in the new version.
 The downtime will simply be the time required for all nodes to stop and start again, which should be less than a minute.
diff --git a/doc/book/quick-start/_index.md b/doc/book/quick-start/_index.md
index feab45f0..ce8cb217 100644
--- a/doc/book/quick-start/_index.md
+++ b/doc/book/quick-start/_index.md
@@ -1,6 +1,6 @@
 +++
 title = "Quick Start"
-weight = 0
+weight = 10
 sort_by = "weight"
 template = "documentation.html"
 +++
diff --git a/doc/book/reference-manual/_index.md b/doc/book/reference-manual/_index.md
index ab1de5e6..1f360e57 100644
--- a/doc/book/reference-manual/_index.md
+++ b/doc/book/reference-manual/_index.md
@@ -1,6 +1,6 @@
 +++
 title = "Reference Manual"
-weight = 5
+weight = 60
 sort_by = "weight"
 template = "documentation.html"
 +++
diff --git a/doc/book/reference-manual/features.md b/doc/book/reference-manual/features.md
index 550504ff..2f8e633a 100644
--- a/doc/book/reference-manual/features.md
+++ b/doc/book/reference-manual/features.md
@@ -35,7 +35,7 @@ This makes setting up and administering storage clusters, we hope, as easy as it
 
 A Garage cluster can very easily evolve over time, as storage nodes are added or removed.
 Garage will automatically rebalance data between nodes as needed to ensure the desired number of copies.
-Read about cluster layout management [here](@/documentation/reference-manual/layout.md).
+Read about cluster layout management [here](@/documentation/operations/layout.md).
 
 ### No RAFT slowing you down
 
diff --git a/doc/book/working-documents/_index.md b/doc/book/working-documents/_index.md
index 8fc170b7..fe79e65d 100644
--- a/doc/book/working-documents/_index.md
+++ b/doc/book/working-documents/_index.md
@@ -1,6 +1,6 @@
 +++
 title = "Working Documents"
-weight = 8
+weight = 90
 sort_by = "weight"
 template = "documentation.html"
 +++