Fix tool_instance_name resolution in save_parameters and support multiple TOPP tool instances

[Copilot]

save_parameters passes tool instance names (e.g., "IDFilter_step1") directly to create_ini, which tries to execute them as binaries and fails. The instance name needs to be resolved back to the real tool name ("IDFilter") before calling create_ini.

Changes

• StreamlitUI.input_TOPP — Added tool_instance_name parameter. Registers instance_name → tool_name mapping in st.session_state["_topp_tool_instance_map"]. Uses instance name for session state keys, real tool name for ini operations.

• ParameterManager.save_parameters — Resolves instance names via the mapping before calling create_ini and loading ini files. Maps ini_key back to real tool name format for param.getValue() lookups. Stores params under instance name in JSON.

• CommandExecutor.run_topp — Added tool_instance_name parameter for JSON param lookup, keeping real tool name for the executable and ini path.

• ParameterManager.get_topp_parameters — Added optional tool_instance_name for instance-aware param retrieval.

Usage

# Two IDFilter instances with independent parameters
self.ui.input_TOPP("IDFilter", tool_instance_name="IDFilter_step1")
self.ui.input_TOPP("IDFilter", tool_instance_name="IDFilter_step2")

# Execution uses real tool name + instance name for param lookup
self.executor.run_topp("IDFilter", input_output={...}, tool_instance_name="IDFilter_step1")
self.executor.run_topp("IDFilter", input_output={...}, tool_instance_name="IDFilter_step2")

All parameters default to backward-compatible behavior when tool_instance_name is omitted.

Original prompt

---

This section details on the original issue you should resolve

<issue_title>[Bug] Issues arising from tool_instance_name implementation: Parameter loading failure and command generation errors</issue_title>
<issue_description>The introduction of tool_instance_name to support multiple instances of the same TOPP tool (e.g., duplicate IDFilter calls) has caused a side effect when executing the save_parameters method.

Specifically, during the execution of the save_parameters loop, the tool_instance_name is being passed into the create_ini method. This results in an invalid tool name causing create_ini to fail.

for tool in current_topp_tools:
            if not self.create_ini(tool):
                # Could not create ini file - skip this tool
                continue
```</issue_description>

<agent_instructions>Please run a deep investigation why this is the case and open a PR with a summary, clearly tracing the error.</agent_instructions>

## Comments on the Issue (you are @copilot in this section)

<comments>
</comments>

• Fixes [Bug] Issues arising from tool_instance_name implementation: Parameter loading failure and command generation errors #353

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