MUCH CRAP from jules and i ;improved agent.docs, add ADR logs, fix/update crates versions, improved other stuff

.github/copilot-instructions.md

@@ -0,0 +1,61 @@
+---
+# Codacy Rules
+Configuration for AI behavior when interacting with Codacy's MCP Server
+
+## CRITICAL: After ANY successful `edit_file` or `reapply` operation
+- YOU MUST IMMEDIATELY run the `codacy_cli_analyze` tool from Codacy's MCP Server for each file that was edited, with:
+ - `rootPath`: set to the workspace path
+ - `file`: set to the path of the edited file
+ - `tool`: leave empty or unset
+- If any issues are found in the new edits, propose and apply fixes for them.
+- > NOTE: Failure to follow this rule is considered a critical error.
+
+## After every response
+- If you made any file edits in this conversation, verify you ran `codacy_cli_analyze` tool from Codacy's MCP Server 
+
+## When there are no Codacy MCP Server tools available, or the MCP Server is not reachable
+- Suggest the user the following troubleshooting steps:
+ - Try to reset the MCP on the extension
+ - If the user is using VSCode, suggest them to review their Copilot > MCP settings in Github, under their organization or personal account. Refer them to Settings > Copilot > Enable MCP servers in Copilot. Suggested URL (https://github.com/settings/copilot/features) or https://github.com/organizations/{organization-name}/settings/copilot/features (This can only be done by their organization admins / owners)
+- If none of the above steps work, suggest the user to contact Codacy support
+
+## Trying to call a tool that needs a rootPath as a parameter
+- Always use the standard, non-URL-encoded file system path
+
+## CRITICAL: Dependencies and Security Checks
+- IMMEDIATELY after ANY of these actions:
+ - Running npm/yarn/pnpm install
+ - Adding dependencies to package.json
+ - Adding requirements to requirements.txt
+ - Adding dependencies to pom.xml
+ - Adding dependencies to build.gradle
+ - Any other package manager operations
+- You MUST run the `codacy_cli_analyze` tool with:
+ - `rootPath`: set to the workspace path
+ - `tool`: set to "trivy"
+ - `file`: leave empty or unset
+- If any vulnerabilities are found because of the newly added packages:
+ - Stop all other operations
+ - Propose and apply fixes for the security issues
+ - Only continue with the original task after security issues are resolved
+- EXAMPLE:
+ - After: npm install react-markdown
+ - Do: Run codacy_cli_analyze with trivy
+ - Before: Continuing with any other tasks
+
+## General
+- Repeat the relevant steps for each modified file.
+- "Propose fixes" means to both suggest and, if possible, automatically apply the fixes.
+- You MUST NOT wait for the user to ask for analysis or remind you to run the tool.
+- Do not run `codacy_cli_analyze` looking for changes in duplicated code or code complexity metrics.
+- Do not run `codacy_cli_analyze` looking for changes in code coverage.
+- Do not try to manually install Codacy CLI using either brew, npm, npx, or any other package manager.
+- If the Codacy CLI is not installed, just run the `codacy_cli_analyze` tool from Codacy's MCP Server.
+- When calling `codacy_cli_analyze`, only send provider, organization and repository if the project is a git repository.
+
+## Whenever a call to a Codacy tool that uses `repository` or `organization` as a parameter returns a 404 error
+- Offer to run the `codacy_setup_repository` tool to add the repository to Codacy
+- If the user accepts, run the `codacy_setup_repository` tool
+- Do not ever try to run the `codacy_setup_repository` tool on your own
+- After setup, immediately retry the action that failed (only retry once)
+---

.github/instructions/codacy.instructions.md

@@ -0,0 +1,65 @@
+---
+    description: Configuration for AI behavior when interacting with Codacy's MCP Server
+    applyTo: '**'
+---
+---
+# Codacy Rules
+Configuration for AI behavior when interacting with Codacy's MCP Server
+
+## CRITICAL: After ANY successful `edit_file` or `reapply` operation
+- YOU MUST IMMEDIATELY run the `codacy_cli_analyze` tool from Codacy's MCP Server for each file that was edited, with:
+ - `rootPath`: set to the workspace path
+ - `file`: set to the path of the edited file
+ - `tool`: leave empty or unset
+- If any issues are found in the new edits, propose and apply fixes for them.
+- > NOTE: Failure to follow this rule is considered a critical error.
+
+## After every response
+- If you made any file edits in this conversation, verify you ran `codacy_cli_analyze` tool from Codacy's MCP Server 
+
+## When there are no Codacy MCP Server tools available, or the MCP Server is not reachable
+- Suggest the user the following troubleshooting steps:
+ - Try to reset the MCP on the extension
+ - If the user is using VSCode, suggest them to review their Copilot > MCP settings in Github, under their organization or personal account. Refer them to Settings > Copilot > Enable MCP servers in Copilot. Suggested URL (https://github.com/settings/copilot/features) or https://github.com/organizations/{organization-name}/settings/copilot/features (This can only be done by their organization admins / owners)
+- If none of the above steps work, suggest the user to contact Codacy support
+
+## Trying to call a tool that needs a rootPath as a parameter
+- Always use the standard, non-URL-encoded file system path
+
+## CRITICAL: Dependencies and Security Checks
+- IMMEDIATELY after ANY of these actions:
+ - Running npm/yarn/pnpm install
+ - Adding dependencies to package.json
+ - Adding requirements to requirements.txt
+ - Adding dependencies to pom.xml
+ - Adding dependencies to build.gradle
+ - Any other package manager operations
+- You MUST run the `codacy_cli_analyze` tool with:
+ - `rootPath`: set to the workspace path
+ - `tool`: set to "trivy"
+ - `file`: leave empty or unset
+- If any vulnerabilities are found because of the newly added packages:
+ - Stop all other operations
+ - Propose and apply fixes for the security issues
+ - Only continue with the original task after security issues are resolved
+- EXAMPLE:
+ - After: npm install react-markdown
+ - Do: Run codacy_cli_analyze with trivy
+ - Before: Continuing with any other tasks
+
+## General
+- Repeat the relevant steps for each modified file.
+- "Propose fixes" means to both suggest and, if possible, automatically apply the fixes.
+- You MUST NOT wait for the user to ask for analysis or remind you to run the tool.
+- Do not run `codacy_cli_analyze` looking for changes in duplicated code or code complexity metrics.
+- Do not run `codacy_cli_analyze` looking for changes in code coverage.
+- Do not try to manually install Codacy CLI using either brew, npm, npx, or any other package manager.
+- If the Codacy CLI is not installed, just run the `codacy_cli_analyze` tool from Codacy's MCP Server.
+- When calling `codacy_cli_analyze`, only send provider, organization and repository if the project is a git repository.
+
+## Whenever a call to a Codacy tool that uses `repository` or `organization` as a parameter returns a 404 error
+- Offer to run the `codacy_setup_repository` tool to add the repository to Codacy
+- If the user accepts, run the `codacy_setup_repository` tool
+- Do not ever try to run the `codacy_setup_repository` tool on your own
+- After setup, immediately retry the action that failed (only retry once)
+---

.gitignore

@@ -7,3 +7,7 @@ Cargo.lock
 /.vs
 .git-credentials
 .gitconfig
+
+
+#Ignore vscode AI rules
+.github\instructions\codacy.instructions.md

Cargo.toml

@@ -8,51 +8,55 @@ license = "MIT"
 repository = "https://github.com/kalisam/amazon_rose_forest_01"
 
 [dependencies]
-tokio = { version = "1.28.0", features = ["full"] }
-serde = { version = "1.0", features = ["derive"] }
-serde_json = "1.0"
-thiserror = "1.0"
-anyhow = "1.0"
-tracing = "0.1"
-tracing-subscriber = "0.3"
-futures = "0.3"
-dashmap = "5.4.0"
-rand = "0.8"
-bytes = "1.4"
-uuid = { version = "1.3", features = ["v4", "serde"] }
-async-trait = "0.1"
-chrono = { version = "0.4", features = ["serde"] }
-hashbrown = "0.14"
-prometheus = "0.13"
-once_cell = "1.18.0"
-rand_distr = "0.4"
-sha2 = "0.10.7"  # Added SHA-2 cryptographic hash functions
-sha3 = { version = "0.10", optional = true }
-blake3 = { version = "1", optional = true }
-serde_bytes = "0.11"
-wide = "0.7"
-warp = "0.3"
-bulletproofs = "4.0.0"
+tokio = { version = "1.47.1", features = ["full"] }
+serde = { version = "1.0.219", features = ["derive"] }
+serde_json = "1.0.142"
+thiserror = "2.0.12"
+anyhow = "1.0.98"
+tracing = "0.1.41"
+tracing-subscriber = "0.3.19"
+futures = "0.3.31"
+dashmap = "6.1.0"
+rand = "0.9.2"
+bytes = "1.10.1"
+uuid = { version = "1.17.0", features = ["v4", "serde"] }
+async-trait = "0.1.88"
+chrono = { version = "0.4.41", features = ["serde"] }
+hashbrown = "0.15.5"
+prometheus = "0.14.0"
+once_cell = "1.21.3"
+rand_distr = "0.5.1"
+sha2 = "0.10.9"  # Added SHA-2 cryptographic hash functions
+sha3 = { version = "0.10.8", optional = true }
+blake3 = { version = "1.8.2", optional = true }
+serde_bytes = "0.11.17"
+wide = "0.7.33"
+reqwest = { version = "0.12.22", features = ["json", "multipart"] }
+warp = { version = "0.4.1", features = ["websocket","server"] }
+
+bulletproofs = "5.0.0"
 ad4m-client = "0.10.1-release-candidate-3"
-sysinfo = "0.28"
+sysinfo = "0.36.1"
 
 
 # Holochain dependencies
-hdk = "0.1.0"
-holo_hash = "0.1.0"
-holochain_zome_types = "0.1.0"
-holochain = { version = "0.1.0", optional = true }
-petgraph = "0.6.3"
-nalgebra = "0.32.2"
-opentelemetry = "0.19.0"
-opentelemetry-otlp = "0.12.0"
+hdk =  "0.5.4"
+hdi = "0.6.4"
+holochain_types = "0.5.4" 
+holo_hash = "0.5.4"
+holochain_zome_types = "0.5.4"
+holochain = { version = "0.5.4", optional = true }
+petgraph = "0.8.2"
+nalgebra = "0.34.0"
+opentelemetry = "0.30.0"
+opentelemetry-otlp = "0.30.0"
 
 [dev-dependencies]
-criterion = "0.4"
-tokio-test = "0.4"
-proptest = "1.1"
-rand = "0.8"
-rand_chacha = "0.3"
+criterion = "0.7.0"
+tokio-test = "0.4.4"
+proptest = "1.7.0"
+rand = "0.9.2"
+rand_chacha = "0.9.0"
 
 [features]
 default = ["sha2"]