Track A.2: vendor libbz2 + 37 fork-only files into pyxis

Configuration moves to make pyxis buildable against vanilla
attermann/microReticulum @ 0.3.0 instead of the fork:

- lib/libbz2/  — pulled from torlando-tech/microReticulum @ ca355e5
  (the previous submodule pin). Used by LXMF compression. Will
  eventually move into the standalone microLXMF library (Track B).
- src-shim/    — the 37 fork-only files NOT already vendored into
  pyxis/lib/ as part of the original split. Includes:
    - LXMF/* (11 files) — to extract as a standalone library (Track B)
    - Cryptography/{BZ2,Ratchet}.{cpp,h} — used by LXMF + RNS 1.x compat
    - Instrumentation/{BootProfiler,MemoryMonitor}.{cpp,h} — pyxis-specific
    - Utilities/{Print,Stream}.{cpp,h} — pyxis logging supplements
    - root: Buffer, BytesPool, ChannelData, Display+Graphics, FileStream,
      FileSystem, MessageBase, ObjectPool, PSRAMAllocator, SegmentAccumulator
- platformio.ini lib_deps: drop the symlink:// to deps/microReticulum/lib/libbz2
  (gone in upstream), add microStore as a github URL dep (vanilla
  upstream needs it for Bytes.h's microStore/Codec.h include).
- platformio.ini build_flags: add -Isrc-shim plus its subdirectories
  so the vendored ../X.h-style includes (rewritten to <X.h>) resolve
  through pyxis's own paths first.

src-shim/* was bulk-rewritten so `#include "../X.h"` (relative to
the fork's src/) becomes `#include <X.h>` resolved via -I deps/microReticulum/src.

Pyxis still doesn't build at this point — the next layer of breakage
is API-level (not file-level): pyxis main.cpp calls fork-only
Identity/LXMRouter/Transport methods that vanilla upstream doesn't
have. See the followup commit's notes / branch description for the
full list.

src-shim/Utilities/Stream.cpp

@@ -0,0 +1,339 @@
+/*
+ Stream.cpp - adds parsing methods to Stream class
+ Copyright (c) 2008 David A. Mellis.  All right reserved.
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 2.1 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+ Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public
+ License along with this library; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301  USA
+
+ Created July 2011
+ parsing functions based on TextFinder library by Michael Margolis
+ */
+
+#ifndef ARDUINO
+
+#include "Stream.h"
+#include "OS.h"
+
+#define PARSE_TIMEOUT 1000  // default number of milli-seconds to wait
+#define NO_SKIP_CHAR  1  // a magic char not found in a valid ASCII numeric field
+
+// private method to read stream with timeout
+int Stream::timedRead()
+{
+    int c;
+    _startMillis = RNS::Utilities::OS::ltime();
+    do {
+        c = read();
+        if(c >= 0) {
+            return c;
+        }
+    } while(RNS::Utilities::OS::ltime() - _startMillis < _timeout);
+    return -1;     // -1 indicates timeout
+}
+
+// private method to peek stream with timeout
+int Stream::timedPeek()
+{
+    int c;
+    _startMillis = RNS::Utilities::OS::ltime();
+    do {
+        c = peek();
+        if(c >= 0) {
+            return c;
+        }
+    } while(RNS::Utilities::OS::ltime() - _startMillis < _timeout);
+    return -1;     // -1 indicates timeout
+}
+
+// returns peek of the next digit in the stream or -1 if timeout
+// discards non-numeric characters
+int Stream::peekNextDigit()
+{
+    int c;
+    while(1) {
+        c = timedPeek();
+        if(c < 0) {
+            return c;    // timeout
+        }
+        if(c == '-') {
+            return c;
+        }
+        if(c >= '0' && c <= '9') {
+            return c;
+        }
+        read();  // discard non-numeric
+    }
+}
+
+// Public Methods
+//////////////////////////////////////////////////////////////
+
+void Stream::setTimeout(unsigned long timeout)  // sets the maximum number of milliseconds to wait
+{
+    _timeout = timeout;
+}
+unsigned long Stream::getTimeout(void) {
+  return _timeout;
+}
+
+// find returns true if the target string is found
+bool  Stream::find(const char *target)
+{
+  return findUntil(target, strlen(target), NULL, 0);
+}
+
+// reads data from the stream until the target string of given length is found
+// returns true if target string is found, false if timed out
+bool Stream::find(const char *target, size_t length)
+{
+  return findUntil(target, length, NULL, 0);
+}
+
+// as find but search ends if the terminator string is found
+bool  Stream::findUntil(const char *target, const char *terminator)
+{
+  return findUntil(target, strlen(target), terminator, strlen(terminator));
+}
+
+// reads data from the stream until the target string of the given length is found
+// search terminated if the terminator string is found
+// returns true if target string is found, false if terminated or timed out
+bool Stream::findUntil(const char *target, size_t targetLen, const char *terminator, size_t termLen)
+{
+  if (terminator == NULL) {
+    MultiTarget t[1] = {{target, targetLen, 0}};
+    return findMulti(t, 1) == 0 ? true : false;
+  } else {
+    MultiTarget t[2] = {{target, targetLen, 0}, {terminator, termLen, 0}};
+    return findMulti(t, 2) == 0 ? true : false;
+  }
+}
+
+int Stream::findMulti( struct Stream::MultiTarget *targets, int tCount) {
+  // any zero length target string automatically matches and would make
+  // a mess of the rest of the algorithm.
+  for (struct MultiTarget *t = targets; t < targets+tCount; ++t) {
+    if (t->len <= 0)
+      return t - targets;
+  }
+
+  while (1) {
+    int c = timedRead();
+    if (c < 0)
+      return -1;
+
+    for (struct MultiTarget *t = targets; t < targets+tCount; ++t) {
+      // the simple case is if we match, deal with that first.
+      if (c == t->str[t->index]) {
+        if (++t->index == t->len)
+          return t - targets;
+        else
+          continue;
+      }
+
+      // if not we need to walk back and see if we could have matched further
+      // down the stream (ie '1112' doesn't match the first position in '11112'
+      // but it will match the second position so we can't just reset the current
+      // index to 0 when we find a mismatch.
+      if (t->index == 0)
+        continue;
+
+      int origIndex = t->index;
+      do {
+        --t->index;
+        // first check if current char works against the new current index
+        if (c != t->str[t->index])
+          continue;
+
+        // if it's the only char then we're good, nothing more to check
+        if (t->index == 0) {
+          t->index++;
+          break;
+        }
+
+        // otherwise we need to check the rest of the found string
+        int diff = origIndex - t->index;
+        size_t i;
+        for (i = 0; i < t->index; ++i) {
+          if (t->str[i] != t->str[i + diff])
+            break;
+        }
+
+        // if we successfully got through the previous loop then our current
+        // index is good.
+        if (i == t->index) {
+          t->index++;
+          break;
+        }
+
+        // otherwise we just try the next index
+      } while (t->index);
+    }
+  }
+  // unreachable
+  return -1;
+}
+
+// returns the first valid (long) integer value from the current position.
+// initial characters that are not digits (or the minus sign) are skipped
+// function is terminated by the first character that is not a digit.
+long Stream::parseInt()
+{
+    return parseInt(NO_SKIP_CHAR); // terminate on first non-digit character (or timeout)
+}
+
+// as above but a given skipChar is ignored
+// this allows format characters (typically commas) in values to be ignored
+long Stream::parseInt(char skipChar)
+{
+    bool isNegative = false;
+    long value = 0;
+    int c;
+
+    c = peekNextDigit();
+    // ignore non numeric leading characters
+    if(c < 0) {
+        return 0;    // zero returned if timeout
+    }
+
+    do {
+        if(c == skipChar) {
+        } // ignore this charactor
+        else if(c == '-') {
+            isNegative = true;
+        } else if(c >= '0' && c <= '9') {    // is c a digit?
+            value = value * 10 + c - '0';
+        }
+        read();  // consume the character we got with peek
+        c = timedPeek();
+    } while((c >= '0' && c <= '9') || c == skipChar);
+
+    if(isNegative) {
+        value = -value;
+    }
+    return value;
+}
+
+// as parseInt but returns a floating point value
+float Stream::parseFloat()
+{
+    return parseFloat(NO_SKIP_CHAR);
+}
+
+// as above but the given skipChar is ignored
+// this allows format characters (typically commas) in values to be ignored
+float Stream::parseFloat(char skipChar)
+{
+    bool isNegative = false;
+    bool isFraction = false;
+    long value = 0;
+    int c;
+    float fraction = 1.0;
+
+    c = peekNextDigit();
+    // ignore non numeric leading characters
+    if(c < 0) {
+        return 0;    // zero returned if timeout
+    }
+
+    do {
+        if(c == skipChar) {
+        } // ignore
+        else if(c == '-') {
+            isNegative = true;
+        } else if(c == '.') {
+            isFraction = true;
+        } else if(c >= '0' && c <= '9') {    // is c a digit?
+            value = value * 10 + c - '0';
+            if(isFraction) {
+                fraction *= 0.1f;
+            }
+        }
+        read();  // consume the character we got with peek
+        c = timedPeek();
+    } while((c >= '0' && c <= '9') || c == '.' || c == skipChar);
+
+    if(isNegative) {
+        value = -value;
+    }
+    if(isFraction) {
+        return value * fraction;
+    } else {
+        return value;
+    }
+}
+
+// read characters from stream into buffer
+// terminates if length characters have been read, or timeout (see setTimeout)
+// returns the number of characters placed in the buffer
+// the buffer is NOT null terminated.
+//
+size_t Stream::readBytes(char *buffer, size_t length)
+{
+    size_t count = 0;
+    while(count < length) {
+        int c = timedRead();
+        if(c < 0) {
+            break;
+        }
+        *buffer++ = (char) c;
+        count++;
+    }
+    return count;
+}
+
+// as readBytes with terminator character
+// terminates if length characters have been read, timeout, or if the terminator character  detected
+// returns the number of characters placed in the buffer (0 means no valid data found)
+
+size_t Stream::readBytesUntil(char terminator, char *buffer, size_t length)
+{
+    if(length < 1) {
+        return 0;
+    }
+    size_t index = 0;
+    while(index < length) {
+        int c = timedRead();
+        if(c < 0 || c == terminator) {
+            break;
+        }
+        *buffer++ = (char) c;
+        index++;
+    }
+    return index; // return number of characters, not including null terminator
+}
+
+std::string Stream::readString()
+{
+    std::string ret;
+    int c = timedRead();
+    while(c >= 0) {
+        ret += (char) c;
+        c = timedRead();
+    }
+    return ret;
+}
+
+std::string Stream::readStringUntil(char terminator)
+{
+    std::string ret;
+    int c = timedRead();
+    while(c >= 0 && c != terminator) {
+        ret += (char) c;
+        c = timedRead();
+    }
+    return ret;
+}
+
+#endif